Isolated human ras- like proteins, nucleic acid molecules encoding these human ras-like proteins , and uses thereof

ABSTRACT

The present invention provides amino acid sequences of polypeptides that are encoded by genes within the human genome, the Ras-like protein polypeptides of the present invention. The present invention specifically provides isolated polypeptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the Ras-like protein polypeptides, and methods of identifying modulators of the Ras-like protein polypeptides.

FIELD OF THE INVENTION

The present invention is in the field of Ras-like proteins that arerelated to the Rab subfamily, recombinant DNA molecules and proteinproduction. The present invention specifically provides a novel Rabprotein alternative splice form and nucleic acid molecules encoding thenovel splice form, all of which are useful in the development of humantherapeutics and diagnostic compositions and methods.

BACKGROUND OF THE INVENTION

Ras-like proteins, particularly members of the Rab subfamilies, are amajor target for drug action and development. Accordingly, it isvaluable to the field of pharmaceutical development to identify andcharacterize previously unknown members of this subfamily of Ras-likeproteins. The present invention advances the state of the art byproviding a previously unidentified human Ras-like proteins that havehomology to members of the Rab subfamilies.

Ras Protein

Ras proteins are small regulatory GTP-binding proteins, or small Gproteins, which belong to the Ras protein superfamily. They aremonomeric GTPases, but their GTPase activity is very slow (less than oneGTP molecule per minute).

Ras proteins are key relays in the signal-transducing cascade induced bythe binding of a ligand to specific receptors such as receptor tyrosinekinases (RTKs), since they trigger the MAP kinase cascade. The ligandcan be a growth factor (epidermal growth factor (EGF), platelet-derivedgrowth factor (PDGF), insulin, an interleukin (IL), granulocytecolony-stimulating factor (G-CSF), granulocyte/macrophagecolony-stimulating factor (GM-CSF).

Ras proteins contain sequences highly conserved during evolution. Theirtertiary structure includes ten loops connecting six strands ofbeta-sheet and five alpha helices.

In mammalians, there are four Ras proteins, which are encoded by Ha-ras,N-ras, Ki-rasA and Ki-rasB genes. They are composed of about 170residues and have a relative molecular mass of 21 kD. Ras proteinscontain covalently attached modified lipids allowing these proteins tobind to the plasma membrane. Ha-Ras has a C-terminal farnesyl group, aC-terminal palmitoyl group and a N-terminal myristoyl group. InKi-Ras(B), a C-terminal polylysine domain replaces the palmitoyl group.

Ras proteins alternate between an inactive form bound to GDP and anactive form bound to GTP. Their activation results from reactionsinduced by a guanine nucleotide-exchange factor (GEF). Theirinactivation results from reactions catalyzed by a GTPase-activatingprotein (GAP).

When a Ras protein is activated by a GEF such as a Sos protein, theN-terminal region of a serine/threonine kinase, called “Raf protein”,can bind to Ras protein. The C-terminal region of the activated Raf thusformed binds to another protein, MEK, and phosphorylates it on bothspecific tyrosine and serine residues. Active MEK phosphorylates andactivates, in turn, a MAP kinase (ERK1 or ERK2), which is also aserine/threonine kinase. This phosphorylation occurs on both specifictyrosine and threonine residues of MAP kinase.

MAP kinase phosphorylates many different proteins, especially nucleartranscription factors (TFs) that regulate expression of many genesduring cell proliferation and differentiation.

Recent researches suggest that, in mammalians, phosphatidyl inositol3′-kinase (PI3-kinase) might be a target of Ras protein, instead of Rafprotein. In certain mutations, the translation of ras genes may produceoncogenic Ras proteins.

Ras-Like Protein

Guanine nucleotide-binding proteins (GTP-binding proteins, or Gproteins) participate in a wide range of regulatory functions includingmetabolism, growth, differentiation, signal transduction, cytoskeletalorganization, and intracellular vesicle transport and secretion. Theseproteins control diverse sets of regulatory pathways in response tohormones, growth factors, neuromodulators, or other signaling molecules.When these molecules bind to transmembrane receptors, signals arepropagated to effector molecules by intracellular signal transducingproteins. Many of these signal-transducing proteins are members of theRas superfamily.

The Ras superfamily is a class of low molecular weight (LMW) GTP-bindingproteins that consist of 21-30 kDa polypeptides. These proteins regulatecell growth, cell cycle control, protein secretion, and intracellularvesicle interaction. In particular, the LMW GTP-binding proteinsactivate cellular proteins by transducing mitogenic signals involved invarious cell functions in response to extracellular signals fromreceptors (Tavitian, A. (1995) C. R. Seances Soc. Biol. Fil. 189:7-12).During this process, the hydrolysis of GTP acts as an energy source aswell as an on-off switch for the GTPase activity of the LMW GTP-bindingproteins.

The Ras superfamily is comprised of five subfamilies: Ras, Rho, Ran,Rab, and ADP-ribosylation factor (ARF). Specifically, Ras genes areessential in the control of cell proliferation. Mutations in Ras geneshave been associated with cancer. Rho proteins control signaltransduction in the process of linking receptors of growth factors toactin polymerization that is necessary for cell division. Rab proteinscontrol the translocation of vesicles to and from membranes for proteinlocalization, protein processing, and secretion. Ran proteins arelocalized to the cell nucleus and play a key role in nuclear proteinimport, control of DNA synthesis, and cell-cycle progression. ARF andARF-like proteins participate in a wide variety of cellular functionsincluding vesicle trafficking, exocrine secretion, regulation ofphospholipase activity, and endocytosis.

Despite their sequence variations, all five subfamilies of the Rassuperfamily share conserved structural features. Four conserved sequenceregions (motifs I-IV) have been studied in the LMW GTP-binding proteins.Motif I is the most variable but has the conserved sequence, GXXXXGK.The lysine residue is essential in interacting with the .beta.- and.gamma.-phosphates of GTP. Motif II, III, and IV contain highlyconserved sequences of DTAGQ, NKXD, and EXSAX, respectively.Specifically, Motif II regulates the binding of gamma-phosphate of GTP;Motif III regulates the binding of GTP; and Motif IV regulates theguanine base of GTP. Most of the membrane-bound LMW GTP-binding proteinsgenerally require a carboxy terminal isoprenyl group for membraneassociation and biological activity. The isoprenyl group is addedposttranslationally through recognition of a terminal cysteine residuealone or a terminal cysteine-aliphatic amino acid-aliphatic aminoacid-any amino acid (CAAX) motif. Additional membrane-binding energy isoften provided by either internal palmitoylation or a carboxy terminalcluster of basic amino acids. The LMW GTP-binding proteins also have avariable effector region, located between motifs I and II, which ischaracterized as the interaction site for guanine nucleotide exchangefactors (GEFs) or GTPase-activating proteins (GAPs). GEFs induce therelease of GDP from the active form of the G protein, whereas GAPsinteract with the inactive form by stimulating the GTPase activity ofthe G protein.

The ARF subfamily has at least 15 distinct members encompassing both ARFand ARF-like proteins. ARF proteins identified to date exhibit highstructural similarity and ADP-ribosylation enhancing activity. Incontrast, several ARF-like proteins lack ADP-ribosylation enhancingactivity and bind GTP differently. An example of ARF-like proteins is arat protein, ARL184. ARL184 has been shown to have a molecular weight of22 kDa and four functional GTP-binding sites (Icard-Liepkalns, C. et al.(1997) Eur. J. Biochem. 246: 388-393). ARL184 is active in both thecytosol and the Golgi apparatus and is closely associated withacetylcholine release, suggesting that ARL184 is a potential regulatoryprotein associated with Ca.sup.2+-dependent release of acetylcholine.

A number of Rho GTP-binding proteins have been identified in plasmamembrane and cytoplasm. These include RhoA, B and C, and D, rhoG, rac 1and 2, G25K-A and B, and TC10 (Hall, A. et al. (1993) Philos. Trans. R.Soc. Lond. (Biol.) 340:267-271). All Rho proteins have a CAAX motif thatbinds a prenyl group and either a palmitoylation site or a basic aminoacid-rich region, suggesting their role in membrane-associatedfunctions. In particular, RhoD is a protein that functions in earlyendosome motility and distribution by inducing rearrangement of actincytoskeleton and cell surface (Murphy, C. et al. (1996) Nature384:427-432). During cell adhesion, the Rho proteins are essential fortriggering focal complex assembly and integrin-dependent signaltransduction (Hotchin, N. A. and Hall, A. (1995) J. Cell Biol.131:1857-1865).

The Ras subfamily proteins already indicated supra are essential intransducing signals from receptor tyrosine kinases (RTKs) to a series ofserine/threonine kinases which control cell growth and differentiation.Mutant Ras proteins, which bind but cannot hydrolyze GTP, arepermanently activated and cause continuous cell proliferation or cancer.TC21, a Ras-like protein, is found to be highly expressed in a humanteratocarcinoma cell line Drivas, G. T. et al. (1990) Mol. Cell. Biol.10: 1793-1798). Rin and Rit are characterized as membrane-binding,Ras-like proteins without the lipid-binding CAAX motif and carboxyterminal cysteine (Lee, C.-H. J. et al. (1996) J. Neurosci. 16:6784-6794). Further, Rin is shown to localize in neurons and havecalcium-dependant calmodulin-binding activity.

Rab Proteins

The novel human protein, and encoding gene, provided by the presentinvention is related to the Rab family of Ras-like proteins and theRab2B isoform in particular. Furthermore, the protein of the presentinvention may be an alternative splice form of a Rab2B protein providedin published patent applications WO200058464 and EP1074617.12472 (seethe amino acid sequence alignment in FIG. 2). Specifically, the proteinof the present invention differs from the art-known protein in the firstexon.

RAB proteins are important for regulating the targeting and fusion ofmembranous vesicles during organelle assembly and transport. RABproteins undergo controlled exchange of GTP for GDP, and they hydrolyzeGTP in a reaction that may regulate the timing and unidirectional natureof these assemblies. Generally, known RAB proteins terminate insequences such as cys-X-cys (e.g., RAB3A), cys-cys (e.g., RAB1A), or asimilar sequence, and generally all are geranylgeranylated.

Rab GTP-binding proteins are similar to YPT1/SEC4 in Saccharomycescerevisiae, which are critical for transport along the exocytic route(Chavrier et al., Mol Cell Biol 1990 December; 10(12):6578-85).Different Rab proteins are presumed to control different steps inmembrane traffic, leading to a high level of diversity and complexitywithin the Rab family (Chavrier et al., Mol Cell Biol 1990 December;10(12):6578-85). The Rab1 gene maps in close viscinity to the ‘wobbler’spinal muscular atrophy gene.

Rab1 and Rab2 from the snail Lymnaea stagnalis share a very high degree(95-97%) of sequence identity with mammalian Rab1 and Rab2 over thefirst 178-191 N-terminal amino acids; however, the C-terminal region isalmost completely divergent, except for the final 2-4 amino acids at theextreme ends. Rab1 was found to be highly expressed in the albumin glandof Lymnaea stagnalis, suggesting an important role in that gland(Agterberg et al., Eur. J. Biochem. 217 (1), 241-246 (1993)).

The tethering factor p115 is a RAB1 effector that binds directly toactivated RAB1. It is thought that RAB1-regulated assembly of functionaleffector-SNARE complexes serves as a conserved molecular mechanism forregulating recognition between different subcellular compartments suchas endoplasmic reticulum and Golgi apparatus (Allan et al., Science 289:444-448, 2000).

GTPases play important roles in a wide variety of cell functions such assignal transduction, cytoskeletal organization, and membranetrafficking. Rab GTPases are particularly important for regulatingcellular membrane dynamics by modulating the activity of effectorproteins that then regulate vesicle trafficking. The Rab8 GTPase playsimportant roles in Golgi to plasma membrane vesicle trafficking. Studieshave suggested that Rab37 plays an important role in mast celldegranulation. Thus, novel human Rab GTPases may be valuable aspotential therapeutic targets for the development of allergy treatments(Masuda et al., FEBS Lett 2000 Mar. 17; 470). Rab15 may act, togetherwith Rab3A, to regulate synaptic vesicle membrane flow within nerveterminals, thereby regulating neurotransmitter release. Rab15 and Rab3Aare low molecular weight GTP-binding proteins. Rab proteins aregenerally comprised of four conserved structural domains necessary forGTP binding, as well as additional domains for membrane localization andeffector protein interactions. Rab15 is expressed primarily in neuraltissues such as the brain and is localized to synaptic vesicles(Elferink et al., J. Biol. Chem. 267 (9), 5768-5775 (1992)).

For a further review of Rab proteins, see Wedemeyer et al., Genomics 32:447-454, 1996 and Zahraoui et al., J. Biol. Chem. 264: 12394-12401,1989.

Due to their importance in human physiology, particularly in regulatingmembrane trafficking, novel human Rab proteins/genes, such as providedby the present invention, are valuable as potential targets for thedevelopment of therapeutics to treat a wide variety ofdiseases/disorders caused or influenced by defects in membranetrafficking. Furthermore, SNPs in Rab genes are valuable markers for thediagnosis, prognosis, prevention, and/or treatment of suchdiseases/disorders.

The discovery of new human Ras-like proteins and the polynucleotidesthat encode them satisfies a need in the art by providing newcompositions that are useful in the diagnosis, prevention, and treatmentof inflammation and disorders associated with cell proliferation andapoptosis.

SUMMARY OF THE INVENTION

The present invention is based in part on the identification of aminoacid sequences of a novel human Rab protein alternative splice form, aswell as other mammalian orthologs thereof. These unique peptidesequences, and nucleic acid sequences that encode these peptides, can beused as models for the development of human therapeutic targets, aid inthe identification of therapeutic proteins, and serve as targets for thedevelopment of human therapeutic agents that modulate Ras-like proteinactivity in cells and tissues that express the Ras-like protein.Experimental data as provided in FIG. 1 indicates expression in humansin germ cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, brain, and leukocytes.

DESCRIPTION OF THE FIGURE SHEETS

FIG. 1 provides the nucleotide sequence of a cDNA molecule that encodesthe Ras-like protein of the present invention. (SEQ ID NO:1) Inaddition, structure and functional information is provided, such as ATGstart, stop and tissue distribution, where available, that allows one toreadily determine specific uses of inventions based on this molecularsequence. Experimental data as provided in FIG. 1 indicates expressionin humans in germ cell tumors, retina, testis, liver/spleen, colon,melanotic melanoma, brain, and leukocytes.

FIG. 2 provides the predicted amino acid sequence of the Ras-likeprotein of the present invention. (SEQ ID NO:2) In addition structureand functional information such as protein family, function, andmodification sites is provided where available, allowing one to readilydetermine specific uses of inventions based on this molecular sequence.

FIG. 3 provides genomic sequences that span the gene encoding theRas-like protein of the present invention. (SEQ ID NO:3) In additionstructure and functional information, such as intron/exon structure,promoter location, etc., is provided where available, allowing one toreadily determine specific uses of inventions based on this molecularsequence.

DETAILED DESCRIPTION OF THE INVENTION General Description

The present invention is based on the sequencing of the human genome.During the sequencing and assembly of the human genome, analysis of thesequence information revealed previously unidentified fragments of thehuman genome that encode peptides that share structural and/or sequencehomology to protein/peptide/domains identified and characterized withinthe art as being a Ras-like protein or part of a Ras-like protein andare related to the Rab subfamily. Utilizing these sequences, additionalgenomic sequences were assembled and transcript and/or cDNA sequenceswere isolated and characterized. Based on this analysis, the presentinvention provides amino acid sequences of a novel human Rab proteinalternative splice form, nucleic acid sequences in the form oftranscript sequences, cDNA sequences and/or genomic sequences thatencode this Rab splice form, tissue distribution of expression, andinformation about the closest art known protein/peptide/domain that hasstructural or sequence homology to the Rab protein of the presentinvention.

In addition to being previously unknown, the peptides that are providedin the present invention are selected based on their ability to be usedfor the development of commercially important products and services.Specifically, the present peptides are selected based on homology and/orstructural relatedness to known Ras-like proteins of the Rab subfamilyand the expression pattern observed. Experimental data as provided inFIG. 1 indicates expression in humans in germ cell tumors, retina,testis, liver/spleen, colon, melanotic melanoma, brain, and leukocytes.The art has clearly established the commercial importance of members ofthis family of proteins and proteins that have expression patternssimilar to that of the present gene. Some of the more specific featuresof the peptides of the present invention, and the uses thereof, aredescribed herein, particularly in the Background of the Invention and inthe annotation provided in the Figures, and/or are known within the artfor each of the known Rab family or subfamily of Ras-like proteins.

Specific Embodiments

Peptide Molecules

The present invention provides nucleic acid sequences that encodeprotein molecules that have been identified as being members of theRas-like protein family and are related to the Rab subfamily (proteinsequences are provided in FIG. 2, transcript/cDNA sequences are providedin FIG. 1 and genomic sequences are provided in FIG. 3). The peptidesequences provided in FIG. 2, as well as the obvious variants describedherein, particularly allelic variants as identified herein and using theinformation in FIG. 3, will be referred herein as the Ras-like proteinsor peptides of the present invention, Ras-like proteins or peptides, orpeptides/proteins of the present invention.

The present invention provides isolated peptide and protein moleculesthat consist of, consist essentially of, or comprise the amino acidsequences of the Ras-like protein polypeptide disclosed in the FIG. 2,(encoded by the nucleic acid molecule shown in FIG. 1, transcript/cDNAor FIG. 3, genomic sequence), as well as all obvious variants of thesepeptides that are within the art to make and use. Some of these variantsare described in detail below.

As used herein, a peptide is said to be “isolated” or “purified” when itis substantially free of cellular material or free of chemicalprecursors or other chemicals. The peptides of the present invention canbe purified to homogeneity or other degrees of purity. The level ofpurification will be based on the intended use. The critical feature isthat the preparation allows for the desired function of the peptide,even if in the presence of considerable amounts of other components.

In some uses, “substantially free of cellular material” includespreparations of the peptide having less than about 30% (by dry weight)other proteins (i.e., contaminating protein), less than about 20% otherproteins, less than about 10% other proteins, or less than about 5%other proteins. When the peptide is recombinantly produced, it can alsobe substantially free of culture medium, i.e., culture medium representsless than about 20% of the volume of the protein preparation.

The language “substantially free of chemical precursors or otherchemicals” includes preparations of the peptide in which it is separatedfrom chemical precursors or other chemicals that are involved in itssynthesis. In one embodiment, the language “substantially free ofchemical precursors or other chemicals” includes preparations of theRas-like protein polypeptide having less than about 30% (by dry weight)chemical precursors or other chemicals, less than about 20% chemicalprecursors or other chemicals, less than about 10% chemical precursorsor other chemicals, or less than about 5% chemical precursors or otherchemicals.

The isolated Ras-like protein polypeptide can be purified from cellsthat naturally express it, purified from cells that have been altered toexpress it (recombinant), or synthesized using known protein synthesismethods. Experimental data as provided in FIG. 1 indicates expression inhumans in germ cell tumors, retina, testis, liver/spleen, colon,melanotic melanoma, brain, and leukocytes. For example, a nucleic acidmolecule encoding the Ras-like protein polypeptide is cloned into anexpression vector, the expression vector introduced into a host cell andthe protein expressed in the host cell. The protein can then be isolatedfrom the cells by an appropriate purification scheme using standardprotein purification techniques. Many of these techniques are describedin detail below.

Accordingly, the present invention provides proteins that consist of theamino acid sequences provided in FIG. 2 (SEQ ID NO:2), for example,proteins encoded by the transcript/cDNA nucleic acid sequences shown inFIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG. 3 (SEQID NO:3). The amino acid sequence of such a protein is provided in FIG.2. A protein consists of an amino acid sequence when the amino acidsequence is the final amino acid sequence of the protein.

The present invention further provides proteins that consist essentiallyof the amino acid sequences provided in FIG. 2 (SEQ ID NO:2), forexample, proteins encoded by the transcript/cDNA nucleic acid sequencesshown in FIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG.3 (SEQ ID NO:3). A protein consists essentially of an amino acidsequence when such an amino acid sequence is present with only a fewadditional amino acid residues, for example from about 1 to about 100 orso additional residues, typically from 1 to about 20 additional residuesin the final protein.

The present invention further provides proteins that comprise the aminoacid sequences provided in FIG. 2 (SEQ ID NO:2), for example, proteinsencoded by the transcript/cDNA nucleic acid sequences shown in FIG. 1(SEQ ID NO:1) and the genomic sequences provided in FIG. 3 (SEQ IDNO:3). A protein comprises an amino acid sequence when the amino acidsequence is at least part of the final amino acid sequence of theprotein. In such a fashion, the protein can be only the peptide or haveadditional amino acid molecules, such as amino acid residues (contiguousencoded sequence) that are naturally associated with it or heterologousamino acid residues/peptide sequences. Such a protein can have a fewadditional amino acid residues or can comprise several hundred or moreadditional amino acids. The preferred classes of proteins that arecomprised of the Ras-like protein polypeptide of the present inventionare the naturally occurring mature proteins. A brief description of howvarious types of these proteins can be made/isolated is provided below.

The Ras-like protein polypeptides of the present invention can beattached to heterologous sequences to form chimeric or fusion proteins.Such chimeric and fusion proteins comprise a Ras-like proteinpolypeptide operatively linked to a heterologous protein having an aminoacid sequence not substantially homologous to the Ras-like proteinpolypeptide. “Operatively linked” indicates that the Ras-like proteinpolypeptide and the heterologous protein are fused in-frame. Theheterologous protein can be fused to the N-terminus or C-terminus of theRas-like protein polypeptide.

In some uses, the fusion protein does not affect the activity of theRas-like protein polypeptide per se. For example, the fusion protein caninclude, but is not limited to, enzymatic fusion proteins, for examplebeta-galactosidase fusions, yeast two-hybrid GAL fusions, poly-Hisfusions, MYC-tagged, HI-tagged and Ig fusions. Such fusion proteins,particularly poly-His fusions, can facilitate the purification ofrecombinant Ras-like protein polypeptide. In certain host cells (e.g.,mammalian host cells), expression and/or secretion of a protein can beincreased by using a heterologous signal sequence.

A chimeric or fusion protein can be produced by standard recombinant DNAtechniques. For example, DNA fragments coding for the different proteinsequences are ligated together in-frame in accordance with conventionaltechniques. In another embodiment, the fusion gene can be synthesized byconventional techniques including automated DNA synthesizers.Alternatively, PCR amplification of gene fragments can be carried outusing anchor primers which give rise to complementary overhangs betweentwo consecutive gene fragments which can subsequently be annealed andre-amplified to generate a chimeric gene sequence (see Ausubel et al.,Current Protocols in Molecular Biology, 1992). Moreover, many expressionvectors are commercially available that already encode a fusion moiety(e.g., a GST protein). A Ras-like protein polypeptide-encoding nucleicacid can be cloned into such an expression vector such that the fusionmoiety is linked in-frame to the Ras-like protein polypeptide.

As mentioned above, the present invention also provides and enablesobvious variants of the amino acid sequence of the peptides of thepresent invention, such as naturally occurring mature forms of thepeptide, allelic/sequence variants of the peptides, non-naturallyoccurring recombinantly derived variants of the peptides, and orthologsand paralogs of the peptides. Such variants can readily be generatedusing art know techniques in the fields of recombinant nucleic acidtechnology and protein biochemistry. It is understood, however, thatvariants exclude any amino acid sequences disclosed prior to theinvention.

Such variants can readily be identified/made using molecular techniquesand the sequence information disclosed herein. Further, such variantscan readily be distinguished from other peptides based on sequenceand/or structural homology to the Ras-like protein polypeptides of thepresent invention. The degree of homology/identity present will be basedprimarily on whether the peptide is a functional variant ornon-functional variant, the amount of divergence present in the paralogfamily, and the evolutionary distance between the orthologs.

To determine the percent identity of two amino acid sequences or twonucleic acid sequences, the sequences are aligned for optimal comparisonpurposes (e.g., gaps can be introduced in one or both of a first and asecond amino acid or nucleic acid sequence for optimal alignment andnon-homologous sequences can be disregarded for comparison purposes). Ina preferred embodiment, the length of a reference sequence aligned forcomparison purposes is at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% ormore of the length of the reference sequence. The amino acid residues ornucleotides at corresponding amino acid positions or nucleotidepositions are then compared. When a position in the first sequence isoccupied by the same amino acid residue or nucleotide as thecorresponding position in the second sequence, then the molecules areidentical at that position (as used herein amino acid or nucleic acid“identity” is equivalent to amino acid or nucleic acid “homology”). Thepercent identity between the two sequences is a function of the numberof identical positions shared by the sequences, taking into account thenumber of gaps, and the length of each gap, which need to be introducedfor optimal alignment of the two sequences.

The comparison of sequences and determination of percent identity andsimilarity between two sequences can be accomplished using amathematical algorithm. (Computational Molecular Biology, Lesk, A. M.,ed., Oxford University Press, New York, 1988; Biocomputing: Informaticsand Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin,H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis inMolecular Biology, von Heinje, G., Academic Press, 1987; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991). In a preferred embodiment, the percent identity betweentwo amino acid sequences is determined using the Needleman and Wunsch(J. Mol. Biol. (48):444-453 (1970)) algorithm which has beenincorporated into the GAP program in the GCG software package (availableat http://www.gcg.com), using either a Blossom 62 matrix or a PAM250matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a lengthweight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, thepercent identity between two nucleotide sequences is determined usingthe GAP program in the GCG software package (Devereux, J., et al.,Nucleic Acids Res. 12(1):387 (1984)) (available at http://www.gcg.com),using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, thepercent identity between two amino acid or nucleotide sequences isdetermined using the algorithm of E. Meyers and W. Miller (CABIOS,4:11-17 (1989)) which has been incorporated into the ALIGN program(version 2.0), using a PAM120 weight residue table, a gap length penaltyof 12 and a gap penalty of 4.

The nucleic acid and protein sequences of the present invention canfurther be used as a “query sequence” to perform a search againstsequence databases to, for example, identify other family members orrelated sequences. Such searches can be performed using the NBLAST andXBLAST programs (version 2.0) of Altschul, et al. (J. Mol. Biol.215:403-10 (1990)). BLAST nucleotide searches can be performed with theNBLAST program, score=100, word length=12 to obtain nucleotide sequenceshomologous to the nucleic acid molecules of the invention. BLAST proteinsearches can be performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to the proteins ofthe invention. To obtain gapped alignments for comparison purposes,Gapped BLAST can be utilized as described in Altschul et al. (NucleicAcids Res. 25(17):3389-3402 (1997)). When utilizing BLAST and gappedBLAST programs, the default parameters of the respective programs (e.g.,XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.

Full-length pre-processed forms, as well as mature processed forms, ofproteins that comprise one of the peptides of the present invention canreadily be identified as having complete sequence identity to one of theRas-like protein polypeptides of the present invention as well as beingencoded by the same genetic locus as the Ras-like protein polypeptideprovided herein. The gene encoding the novel Rab protein of the presentinvention is located on a genome component that has been mapped to humanchromosome 14 (as indicated in FIG. 3), which is supported by multiplelines of evidence, such as STS and BAC map data.

Allelic variants of a Ras-like protein polypeptide can readily beidentified as being a human protein having a high degree (significant)of sequence homology/identity to at least a portion of the Ras-likeprotein polypeptide as well as being encoded by the same genetic locusas the Ras-like protein polypeptide provided herein. Genetic locus canreadily be determined based on the genomic information provided in FIG.3, such as the genomic sequence mapped to the reference human. The geneencoding the novel Rab protein of the present invention is located on agenome component that has been mapped to human chromosome 14 (asindicated in FIG. 3), which is supported by multiple lines of evidence,such as STS and BAC map data As used herein, two proteins (or a regionof the proteins) have significant homology when the amino acid sequencesare typically at least about 70-80%, 80-90%, and more typically at leastabout 90-95% or more homologous. A significantly homologous amino acidsequence, according to the present invention, will be encoded by anucleic acid sequence that will hybridize to a Ras-like proteinpolypeptide encoding nucleic acid molecule under stringent conditions asmore fully described below.

Paralogs of a Ras-like protein polypeptide can readily be identified ashaving some degree of significant sequence homology/identity to at leasta portion of the Ras-like protein polypeptide, as being encoded by agene from humans, and as having similar activity or function. Twoproteins will typically be considered paralogs when the amino acidsequences are typically at least about 40-50%, 50-60%, and moretypically at least about 60-70% or more homologous through a givenregion or domain. Such paralogs will be encoded by a nucleic acidsequence that will hybridize to a Ras-like protein polypeptide encodingnucleic acid molecule under moderate to stringent conditions as morefully described below.

Orthologs of a Ras-like protein polypeptide can readily be identified ashaving some degree of significant sequence homology/identity to at leasta portion of the Ras-like protein polypeptide as well as being encodedby a gene from another organism. Preferred orthologs will be isolatedfrom mammals, preferably primates, for the development of humantherapeutic targets and agents. Such orthologs will be encoded by anucleic acid sequence that will hybridize to a Ras-like proteinpolypeptide encoding nucleic acid molecule under moderate to stringentconditions, as more fully described below, depending on the degree ofrelatedness of the two organisms yielding the proteins.

Non-naturally occurring variants of the Ras-like protein polypeptides ofthe present invention can readily be generated using recombinanttechniques. Such variants include, but are not limited to deletions,additions and substitutions in the amino acid sequence of the Ras-likeprotein polypeptide. For example, one class of substitutions isconserved amino acid substitutions. Such substitutions are those thatsubstitute a given amino acid in a Ras-like protein polypeptide byanother amino acid of like characteristics. Typically seen asconservative substitutions are the replacements, one for another, amongthe aliphatic amino acids Ala, Val, Leu, and Ile; interchange of thehydroxyl residues Ser and Thr, exchange of the acidic residues Asp andGlu, substitution between the amide residues Asn and Gln, exchange ofthe basic residues Lys and Arg, replacements among the aromatic residuesPhe, Tyr, and the like. Guidance concerning which amino acid changes arelikely to be phenotypically silent are found in Bowie et al., Science247:1306-1310 (1990).

Variant Ras-like protein polypeptides can be fully functional or canlack function in one or more activities. Fully functional variantstypically contain only conservative variations or variations innon-critical residues or in non-critical regions. Functional variantscan also contain substitution of similar amino acids that result in nochange or an insignificant change in function. Alternatively, suchsubstitutions may positively or negatively affect function to somedegree.

Non-functional variants typically contain one or more non-conservativeamino acid substitutions, deletions, insertions, inversions, ortruncation or a substitution, insertion, inversion, or deletion in acritical residue or critical region.

Amino acids that are essential for function can be identified by methodsknown in the art, such as site-directed mutagenesis or alanine-scanningmutagenesis (Cunningham et al., Science 244:1081-1085 (1989)). Thelatter procedure introduces single alanine mutations at every residue inthe molecule. The resulting mutant molecules are then tested forbiological activity such as receptor binding or in vitro proliferativeactivity. Sites that are critical for ligand-receptor binding can alsobe determined by structural analysis such as crystallography, nuclearmagnetic resonance, or photoaffinity labeling (Smith et al., J. Mol.Biol. 224:899-904 (1992); de Vos et al. Science 255:306-312 (1992)).

The present invention further provides fragments of the Ras-like proteinpolypeptides, in addition to proteins and peptides that comprise andconsist of such fragments. Particularly those comprising the residuesidentified in FIG. 2. The fragments to which the invention pertains,however, are not to be construed as encompassing fragments that havebeen disclosed publicly prior to the present invention.

As used herein, a fragment comprises at least 8, 10, 12, 14, 16 or morecontiguous amino acid residues from a Ras-like protein polypeptide. Suchfragments can be chosen based on the ability to retain one or more ofthe biological activities of the Ras-like protein polypeptide, or can bechosen for the ability to perform a function, e.g., act as an immunogen.Particularly important fragments are biologically active fragments,peptides that are, for example about 8 or more amino acids in length.Such fragments will typically comprise a domain or motif of the Ras-likeprotein polypeptide, e.g., active site. Further, possible fragmentsinclude, but are not limited to, domain or motif containing fragments,soluble peptide fragments, and fragments containing immunogenicstructures. Predicted domains and functional sites are readilyidentifiable by computer programs well known and readily available tothose of skill in the art (e.g., PROSITE, HMMer, eMOTIF, etc.). Theresults of one such analysis are provided in FIG. 2.

Polypeptides often contain amino acids other than the 20 amino acidscommonly referred to as the 20 naturally occurring amino acids. Further,many amino acids, including the terminal amino acids, may be modified bynatural processes, such as processing and other post-translationalmodifications, or by chemical modification techniques well known in theart. Common modifications that occur naturally in Ras-like proteinpolypeptides are described in basic texts, detailed monographs, and theresearch literature, and they are well known to those of skill in theart (some of these features are identified in FIG. 2).

Known modifications include, but are not limited to, acetylation,acylation, ADP-ribosylation, amidation, covalent attachment of flavin,covalent attachment of a heme moiety, covalent attachment of anucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, demethylation,formation of covalent crosslinks, formation of cystine, formation ofpyroglutamate, formylation, gamma carboxylation, glycosylation, GPIanchor formation, hydroxylation, iodination, methylation,myristoylation, oxidation, proteolytic processing, phosphorylation,prenylation, racemization, selenoylation, sulfation, transfer-RNAmediated addition of amino acids to proteins such as arginylation, andubiquitination.

Such modifications are well known to those of skill in the art and havebeen described in great detail in the scientific literature. Severalparticularly common modifications, glycosylation, lipid attachment,sulfation, gamma-carboxylation of glutamic acid residues, hydroxylationand ADP-ribosylation, for instance, are described in most basic texts,such as Proteins—Structure and Molecular Properties, 2nd Ed., T. E.Creighton, W. H. Freeman and Company, New York (1993). Many detailedreviews are available on this subject, such as by Wold, F.,Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed.,Academic Press, New York 1-12 (1983); Seifter et al. (Meth. Enzymol.182: 626-646 (1990)) and Rattan et al. (Ann. N.Y. Acad. Sci. 663:48-62(1992)).

Accordingly, the Ras-like protein polypeptides of the present inventionalso encompass derivatives or analogs in which a substituted amino acidresidue is not one encoded by the genetic code, in which a substituentgroup is included, in which the mature Ras-like protein polypeptide isfused with another compound, such as a compound to increase thehalf-life of the Ras-like protein polypeptide (for example, polyethyleneglycol), or in which the additional amino acids are fused to the matureRas-like protein polypeptide, such as a leader or secretory sequence ora sequence for purification of the mature Ras-like protein polypeptide,or a pro-protein sequence.

Protein/Peptide Uses

The proteins of the present invention can be used in assays to determinethe biological activity of the protein, including in a panel of multipleproteins for high-throughput screening; to raise antibodies or to elicitanother immune response; as a reagent (including the labeled reagent) inassays designed to quantitatively determine levels of the protein (orits ligand or receptor) in biological fluids; and as markers for tissuesin which the corresponding protein is preferentially expressed (eitherconstitutively or at a particular stage of tissue differentiation ordevelopment or in a disease state). Where the protein binds orpotentially binds to another protein (such as, for example, in areceptor-ligand interaction), the protein can be used to identify thebinding partner so as to develop a system to identify inhibitors of thebinding interaction. Any or all of these research utilities are capableof being developed into reagent grade or kit format forcommercialization as research products.

Methods for performing the uses listed above are well known to thoseskilled in the art. References disclosing such methods include“Molecular Cloning: A Laboratory Manual”, 2d ed., Cold Spring HarborLaboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds.,1989, and “Methods in Enzymology: Guide to Molecular CloningTechniques”, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.

The potential uses of the peptides of the present invention are basedprimarily on the source of the protein as well as the class/action ofthe protein. For example, Ras-like proteins isolated from humans andtheir human/mammalian orthologs serve as targets for identifying agentsfor use in mammalian therapeutic applications, e.g. a human drug,particularly in modulating a biological or pathological response in acell or tissue that expresses the Ras-like protein. Experimental data asprovided in FIG. 1 indicates that Ras-like proteins of the presentinvention are expressed in humans in germ cell tumors, retina, testis,liver/spleen, colon, melanotic melanoma, and brain, as indicated byvirtual northern blot analysis. In addition, PCR-based tissue screeningpanels indicates expression in leukocytes. A large percentage ofpharmaceutical agents are being developed that modulate the activity ofRas-like proteins, particularly members of the Rab subfamily (seeBackground of the Invention). The structural and functional informationprovided in the Background and Figures provide specific and substantialuses for the molecules of the present invention, particularly incombination with the expression information provided in FIG. 1.Experimental data as provided in FIG. 1 indicates expression in humansin germ cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, brain, and leukocytes. Such uses can readily be determinedusing the information provided herein, that which is known in the art,and routine experimentation.

The proteins of the present invention (including variants and fragmentsthat may have been disclosed prior to the present invention) are usefulfor biological assays related to Ras-like proteins that are related tomembers of the Rab subfamily. Such assays involve any of the knownRas-like protein functions or activities or properties useful fordiagnosis and treatment of Ras-like protein-related conditions that arespecific for the subfamily of Ras-like proteins that the one of thepresent invention belongs to, particularly in cells and tissues thatexpress the Ras-like protein. Experimental data as provided in FIG. 1indicates that Ras-like proteins of the present invention are expressedin humans in germ cell tumors, retina, testis, liver/spleen, colon,melanotic melanoma, and brain, as indicated by virtual northern blotanalysis. In addition, PCR-based tissue screening panels indicatesexpression in leukocytes.

The proteins of the present invention are also useful in drug screeningassays, in cell-based or cell-free systems. Cell-based systems can benative, i.e., cells that normally express the Ras-like protein, as abiopsy or expanded in cell culture. Experimental data as provided inFIG. 1 indicates expression in humans in germ cell tumors, retina,testis, liver/spleen, colon, melanotic melanoma, brain, and leukocytes.In an alternate embodiment, cell-based assays involve recombinant hostcells expressing the Ras-like protein.

The polypeptides can be used to identify compounds that modulateRas-like protein activity. Both the Ras-like protein of the presentinvention and appropriate variants and fragments can be used inhigh-throughput screens to assay candidate compounds for the ability tobind to the Ras-like protein. These compounds can be further screenedagainst a functional Ras-like protein to determine the effect of thecompound on the Ras-like protein activity. Further, these compounds canbe tested in animal or invertebrate systems to determineactivity/effectiveness. Compounds can be identified that activate(agonist) or inactivate (antagonist) the Ras-like protein to a desireddegree.

Therefore, in one embodiment, Rab or a fragment or derivative thereofmay be administered to a subject to prevent or treat a disorderassociated with an increase in apoptosis. Such disorders include, butare not limited to, AIDS and other infectious or geneticimmunodeficiencies, neurodegenerative diseases such as Alzheimer'sdisease, Parkinson's disease, amyotrophic lateral sclerosis, retinitispigmentosa, and cerebellar degeneration, myelodysplastic syndromes suchas aplastic anemia, ischemic injuries such as myocardial infarction,stroke, and reperfusion injury, toxin-induced diseases such asalcohol-induced liver damage, cirrhosis, and lathyrism, wasting diseasessuch as cachexia, viral infections such as those caused by hepatitis Band C, and osteoporosis.

In another embodiment, a pharmaceutical composition comprising Rab maybe administered to a subject to prevent or treat a disorder associatedwith increased apoptosis including, but not limited to, those listedabove.

In still another embodiment, an agonist which is specific for Rab may beadministered to prevent or treat a disorder associated with increasedapoptosis including, but not limited to, those listed above.

In a further embodiment, a vector capable of expressing Rab, or afragment or a derivative thereof, may be used to prevent or treat adisorder associated with increased apoptosis including, but not limitedto, those listed above.

In cancer, where Rab promotes cell proliferation, it is desirable-todecrease its activity. Therefore, in one embodiment, an antagonist ofRab may be administered to a subject to prevent or treat cancerincluding, but not limited to, adenocarcinoma, leukemia, lymphoma,melanoma, myeloma, sarcoma, and teratocarcinoma, and, in particular,cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast,cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney,liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate,salivary glands, skin, spleen, testis, thymus, thyroid, and uterus. Inone aspect, an antibody specific for Rab may be used directly as anantagonist, or indirectly as a targeting or delivery mechanism forbringing a pharmaceutical agent to cells or tissue which express Rab.

In another embodiment, a vector expressing the complement of thepolynucleotide encoding Rab may be administered to a subject to preventor treat a cancer including, but not limited to, the types of cancerlisted above.

In inflammation, where Rab promotes cell proliferation, it is desirableto decrease its activity. Therefore, in one embodiment, an antagonist ofRab may be administered to a subject to prevent or treat aninflammation. Disorders associated with inflammation include, but arenot limited to, Addison's disease, adult respiratory distress syndrome,allergies, anemia, asthma, atherosclerosis, bronchitis, cholecystitis,Crohn's disease, ulcerative colitis, atopic dermatitis, dermatomyositis,diabetes mellitus, emphysema, atrophic gastritis, glomerulonephritis,gout, Graves' disease, hypereosinophilia, irritable bowel syndrome,lupus erythematosus, multiple sclerosis, myasthenia gravis, myocardialor pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis,polymyositis, rheumatoid arthritis, scleroderma, Sjogren's syndrome, andautoimmune thyroiditis; complications of cancer, hemodialysis,extracorporeal circulation; viral, bacterial, fungal, parasitic,protozoal, and helminthic infections and trauma In one aspect, anantibody specific for Rab may be used directly as an antagonist, orindirectly as a targeting or delivery mechanism for bringing apharmaceutical agent to cells or tissue which express Rab.

Further, the Ras-like protein polypeptides can be used to screen acompound for the ability to stimulate or inhibit interaction between theRas-like protein and a molecule that normally interacts with theRas-like protein, e.g. a ligand or a component of the signal pathwaythat the Ras-like protein normally interacts. Such assays typicallyinclude the steps of combining the Ras-like protein with a candidatecompound under conditions that allow the Ras-like protein, or fragment,to interact with the target molecule, and to detect the formation of acomplex between the protein and the target or to detect the biochemicalconsequence of the interaction with the Ras-like protein and the target,such as any of the associated effects of signal transduction.

Candidate compounds include, for example, 1>peptides such as solublepeptides, including Ig-tailed fusion peptides and members of randompeptide libraries (see, e.g., Lam et al., Nature 354:82-84 (1991);Houghten et al., Nature 354:84-86 (1991)) and combinatorialchemistry-derived molecular libraries made of D- and/or L-configurationamino acids; 2) phosphopeptides (e.g., members of random and partiallydegenerate, directed phosphopeptide libraries, see, e.g., Songyang etal., Cell 72:767-778 (1993)); 3) antibodies (e.g., polyclonal,monoclonal, humanized, anti-idiotypic, chimeric, and single chainantibodies as well as Fab, F(ab′)₂, Fab expression library fragments,and epitope-binding fragments of antibodies); and 4) small organic andinorganic molecules (e.g., molecules obtained from combinatorial andnatural product libraries). (Hodgson, Bio/technology, 1992, Sep. 10(9);973-80).

One candidate compound is a soluble fragment of the Ras-like proteinthat competes for ligand binding. Other candidate compounds includemutant Ras-like proteins or appropriate fragments containing mutationsthat affect Ras-like protein function and thus compete for ligand.Accordingly, a fragment that competes for ligand, for example with ahigher affinity, or a fragment that binds ligand but does not allowrelease, is within the scope of the invention.

The invention further includes other end point assays to identifycompounds that modulate (stimulate or inhibit) Ras-like proteinactivity. The assays typically involve an assay of events in theRas-like protein mediated signal transduction pathway that indicateRas-like protein activity. Thus, the phosphorylation of a protein/ligandtarget, the expression of genes that are up- or down-regulated inresponse to the Ras-like protein dependent signal cascade can beassayed. In one embodiment, the regulatory region of such genes can beoperably linked to a marker that is easily detectable, such asluciferase. Alternatively, phosphorylation of the Ras-like protein, or aRas-like protein target, could also be measured.

Any of the biological or biochemical functions mediated by the Ras-likeprotein can be used as an endpoint assay. These include all of thebiochemical or biochemical/biological events described herein, in thereferences cited herein, incorporated by reference for these endpointassay targets, and other functions known to those of ordinary skill inthe art.

Binding and/or activating compounds can also be screened by usingchimeric Ras-like proteins in which any of the protein's domains, orparts thereof, can be replaced by heterologous domains or subregions.Accordingly, a different set of signal transduction components isavailable as an end-point assay-for activation. This allows for assaysto be performed in other than the specific host cell from which theRas-like protein is derived.

The Ras-like protein polypeptide of the present invention is also usefulin competition binding assays in methods designed to discover compoundsthat interact with the Ras-like protein. Thus, a compound is exposed toa Ras-like protein polypeptide under conditions that allow the compoundto bind or to otherwise interact with the polypeptide. Soluble Ras-likeprotein polypeptide is also added to the mixture. If the test compoundinteracts with the soluble Ras-like protein polypeptide, it decreasesthe amount of complex formed or activity from the Ras-like proteintarget. This type of assay is particularly useful in cases in whichcompounds are sought that interact with specific regions of the Ras-likeprotein. Thus, the soluble polypeptide that competes with the targetRas-like protein region is designed to contain peptide sequencescorresponding to the region of interest.

To perform cell free drug screening assays, it is sometimes desirable toimmobilize either the Ras-like protein, or fragment, or its targetmolecule to facilitate separation of complexes from uncomplexed forms ofone or both of the proteins, as well as to accommodate automation of theassay.

Techniques for immobilizing proteins on matrices can be used in the drugscreening assays. In one embodiment, a fusion protein can be providedwhich adds a domain that allows the protein to be bound to a matrix. Forexample, glutathione-S-transferase/15625 fusion proteins can be adsorbedonto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtitre plates, which are then combined withthe cell lysates (e.g., ³⁵S-labeled) and the candidate compound, and themixture incubated under conditions conducive to complex formation (e.g.,at physiological conditions for salt and pH). Following incubation, thebeads are washed to remove any unbound label, and the matrix immobilizedand radiolabel determined directly, or in the supernatant after thecomplexes are dissociated. Alternatively, the complexes can bedissociated from the matrix, separated by SDS-PAGE, and the level ofRas-like protein-binding protein found in the bead fraction quantitatedfrom the gel using standard electrophoretic techniques. For example,either the polypeptide or its target molecule can be immobilizedutilizing conjugation of biotin and streptavidin with techniques wellknown in the art. Alternatively, antibodies reactive with the proteinbut which do not interfere with binding of the protein to its targetmolecule can be derivatized to the wells of the plate, and the proteintrapped in the wells by antibody conjugation. Preparations of a Ras-likeprotein-binding protein and a candidate compound are incubated in theRas-like protein-presenting wells and the amount of complex trapped inthe well can be quantitated. Methods for detecting such complexes, inaddition to those described above for the GST-immobilized complexes,include immunodetection of complexes using antibodies reactive with theRas-like protein target molecule, or which are reactive with Ras-likeprotein and compete with the target molecule, as well as enzyme-linkedassays which rely on detecting an enzymatic activity associated with thetarget molecule.

Agents that modulate one of the Ras-like proteins of the presentinvention can be identified using one or more of the above assays, aloneor in combination. It is generally preferable to use a cell-based orcell free system first and then confirm activity in an animal/insectmodel system. Such model systems are well known in the art and canreadily be employed in this context.

Modulators of Ras-like protein activity identified according to thesedrug screening assays can be used to treat a subject with a disordermediated by the Ras-like protein associated pathway, by treating cellsthat express the Ras-like protein. Experimental data as provided in FIG.1 indicates expression in humans in germ cell tumors, retina, testis,liver/spleen, colon, melanotic melanoma, brain, and leukocytes. Thesemethods of treatment include the steps of administering the modulatorsof protein activity in a pharmaceutical composition as described herein,to a subject in need of such treatment.

In yet another aspect of the invention, the Ras-like proteins can beused as “bait proteins” in a two-hybrid assay or three-hybrid assay(see, e.g., U.S. Pat. No. 5,283,317; Zervos et al., Cell 72:223-232(1993); Madura et al., J. Biol. Chem. 268:12046-12054 (1993); Bartel etal., Biotechniques 14:920-924 (1993); Iwabuchi et al., Oncogene8:1693-1696 (1993); and Brent WO94/10300), to identify other proteinsthat bind to or interact with the Ras-like protein and are involved inRas-like protein activity. Such Ras-like protein-binding proteins arealso likely to be involved in the propagation of signals by the Ras-likeproteins or Ras-like protein targets as, for example, downstreamelements of a Ras-like protein-mediated signaling pathway, e.g., a painsignaling pathway. Alternatively, such Ras-like protein-binding proteinsare likely to be Ras-like protein inhibitors.

The two-hybrid system is based on the modular nature of mosttranscription factors, which consist of separable DNA-binding andactivation domains. Briefly, the assay utilizes two different DNAconstructs. In one construct, the gene that codes for a Ras-like proteinis fused to a gene encoding the DNA binding domain of a knowntranscription factor (e.g., GAL-4). In the other construct, a DNAsequence, from a library of DNA sequences, that encodes an unidentifiedprotein (“prey” or “sample”) is fused to a gene that codes for theactivation domain of the known transcription factor. If the “bait” andthe “prey” proteins are able to interact, in vivo, forming a Ras-likeprotein-dependent complex, the DNA-binding and activation domains of thetranscription factor are brought into close proximity. This proximityallows transcription of a reporter gene (e.g., LacZ) which is operablylinked to a transcriptional regulatory site responsive to thetranscription factor. Expression of the reporter gene can be detectedand cell colonies containing the functional transcription factor can beisolated and used to obtain the cloned gene which encodes the proteinwhich interacts with the Ras-like protein.

This invention further pertains to novel agents identified by theabove-described screening assays. Accordingly, it is within the scope ofthis invention to further use an agent identified as described herein inan appropriate animal model. For example, an agent identified asdescribed herein (e.g., a Ras-like protein modulating agent, anantisense Ras-like protein nucleic acid molecule, a Ras-likeprotein-specific antibody, or a Ras-like protein-binding partner) can beused in an animal or insect model to determine the efficacy, toxicity,or side effects of treatment with such an agent. Alternatively, an agentidentified as described herein can be used in an animal or insect modelto determine the mechanism of action of such an agent. Furthermore, thisinvention pertains to uses of novel agents identified by theabove-described screening assays for treatments as described herein.

The Ras-like proteins of the present invention are also useful toprovide a target for diagnosing a disease or predisposition to a diseasemediated by the peptide, Accordingly, the invention provides methods fordetecting the presence, or levels of, the protein (or encoding mRNA) ina cell, tissue, or organism. Experimental data as provided in FIG. 1indicates expression in humans in germ cell tumors, retina, testis,liver/spleen, colon, melanotic melanoma, brain, and leukocytes. Themethod involves contacting a biological sample with a compound capableof interacting with the receptor protein such that the interaction canbe detected. Such an assay can be provided in a single detection formator a multi-detection format such as an antibody chip array.

One agent for detecting a protein in a sample is an antibody capable ofselectively binding to protein. A biological sample includes tissues,cells and biological fluids isolated from a subject, as well as tissues,cells, and fluids present within a subject.

The peptides also are useful to provide a target for diagnosing adisease or predisposition to a disease mediated by the peptide,Accordingly, the invention provides methods for detecting the presence,or levels of, the protein in a cell, tissue, or organism. The methodinvolves contacting a biological sample with a compound capable ofinteracting with the receptor protein such that the interaction can bedetected.

The peptides of the present invention also provide targets fordiagnosing active disease, or predisposition to a disease, in a patienthaving a variant peptide. Thus, the peptide can be isolated from abiological sample and assayed for the presence of a genetic mutationthat results in translation of an aberrant peptide. This includes aminoacid substitution, deletion, insertion, rearrangement, (as the result ofaberrant splicing events), and inappropriate post-translationalmodification. Analytic methods include altered electrophoretic mobility,altered tryptic peptide digest, altered receptor activity in cell-basedor cell-free assay, alteration in ligand or antibody-binding pattern,altered isoelectric point, direct amino acid sequencing, and any otherof the known assay techniques useful for detecting mutations in aprotein. Such an assay can be provided in a single detection format or amulti-detection format such as an antibody chip array.

In vitro techniques for detection of peptide include enzyme linkedimmunosorbent assays (ELISAs), Western blots, immunoprecipitations, andimmunofluorescence using a detection reagents, such as an antibody orprotein binding agent. Alternatively, the peptide can be detected invivo in a subject by introducing into the subject a labeled anti-peptideantibody. For example, the antibody can be labeled with a radioactivemarker whose presence and location in a subject can be detected bystandard imaging techniques. Particularly useful are methods that detectthe allelic variant of a peptide expressed in a subject and methodswhich detect fragments of a peptide in a sample.

The peptides are also useful in pharmacogenomic analysis.Pharmacogenomics deal with clinically significant hereditary variationsin the response to drugs due to altered drug disposition and abnormalaction in affected persons. See, e.g., Eichelbaum, M. (Clin. Exp.Pharmacol. Physiol. 23(10-11):983-985 (1996)), and Linder, M. W. (Clin.Chem. 43(2):254-266 (1997)). The clinical outcomes of these variationsresult in severe toxicity of therapeutic drugs in certain individuals ortherapeutic failure of drugs in certain individuals as a result ofindividual variation in metabolism. Thus, the genotype of the individualcan determine the way a therapeutic compound acts on the body or the waythe body metabolizes the compound. Further, the activity of drugmetabolizing enzymes effects both the intensity and duration of drugaction. Thus, the pharmacogenomics of the individual permit theselection of effective compounds and effective dosages of such compoundsfor prophylactic or therapeutic treatment based on the individual'sgenotype. The discovery of genetic polymorphisms in some drugmetabolizing enzymes has explained why some patients do not obtain theexpected drug effects, show an exaggerated drug effect, or experienceserious toxicity from standard drug dosages. Polymorphisms can beexpressed in the phenotype of the extensive metabolizer and thephenotype of the poor metabolizer. Accordingly, genetic polymorphism maylead to allelic protein variants of the receptor protein in which one ormore of the receptor functions in one population is different from thosein another population. The peptides thus allow a target to ascertain agenetic predisposition that can affect treatment modality. Thus, in aligand-based treatment, polymorphism may give rise to amino terminalextracellular domains and/or other ligand-binding regions that are moreor less active in ligand binding, and receptor activation. Accordingly,ligand dosage would necessarily be modified to maximize the therapeuticeffect within a given population containing a polymorphism. As analternative to genotyping, specific polymorphic peptides could beidentified.

The peptides are also useful for treating a disorder characterized by anabsence of, inappropriate, or unwanted expression of the protein.Experimental data as provided in FIG. 1 indicates expression in humansin germ cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, brain, and leukocytes. Accordingly, methods for treatmentinclude the use of the Ras-like protein or fragments.

Antibodies

The invention also provides antibodies that selectively bind to one ofthe peptides of the present invention, a protein comprising such apeptide, as well as variants and fragments thereof. As used herein, anantibody selectively binds a target peptide when it binds the targetpeptide and does not significantly bind to unrelated proteins. Anantibody is still considered to selectively bind a peptide even if italso binds to other proteins that are not substantially homologous withthe target peptide so long as such proteins share homology with afragment or domain of the peptide target of the antibody. In this case,it would be understood that antibody binding to the peptide is stillselective despite some degree of cross-reactivity.

As used herein, an antibody is defined in terms consistent with thatrecognized within the art: they are multi-subunit proteins produced by amammalian organism in response to an antigen challenge. The antibodiesof the present invention include polyclonal antibodies and monoclonalantibodies, as well as fragments of such antibodies, including, but notlimited to, Fab or F(ab′)₂, and Fv fragments.

Many methods are known for generating and/or identifying antibodies to agiven target peptide. Several such methods are described by Harlow,Antibodies, Cold Spring Harbor Press, (1989).

In general, to generate antibodies, an isolated peptide is used as animmunogen and is administered to a mammalian organism, such as a rat,rabbit or mouse. The full-length protein, an antigenic peptide fragmentor a fusion protein can be used. Particularly important fragments arethose covering functional domains, such as the domains identified inFIG. 2, and domain of sequence homology or divergence amongst thefamily, such as those that can readily be identified using proteinalignment methods and as presented in the Figures.

Antibodies are preferably prepared from regions or discrete fragments ofthe Ras-like proteins. Antibodies can be prepared from any region of thepeptide as described herein. However, preferred regions will includethose involved in function/activity and/or receptor/binding partnerinteraction. FIG. 2 can be used to identify particularly importantregions while sequence alignment can be used to identify conserved andunique sequence fragments.

An antigenic fragment will typically comprise at least 8 contiguousamino acid residues. The antigenic peptide can comprise, however, atleast 10, 12, 14, 16 or more amino acid residues. Such fragments can beselected on a physical property, such as fragments correspond to regionsthat are located on the surface of the protein, e.g., hydrophilicregions or can be selected based on sequence uniqueness (see FIG. 2).

Detection of an antibody of the present invention can be facilitated bycoupling (i.e., physically linking) the antibody to a detectablesubstance. Examples of detectable substances include various enzymes,prosthetic groups, fluorescent materials, luminescent materials,bioluminescent materials, and radioactive materials. Examples ofsuitable enzymes include horseradish peroxidase, alkaline phosphatase,β-galactosidase, or acetylcholinesterase; examples of suitableprosthetic group complexes include streptavidin/biotin andavidin/biotin; examples of suitable fluorescent materials includeumbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine,dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; anexample of a luminescent material includes luminol; examples ofbioluminescent materials include luciferase, luciferin, and aequorin,and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S,or ³H.

Antibody Uses

The antibodies can be used to isolate one of the proteins of the presentinvention by standard techniques, such as affinity chromatography orimmunoprecipitation. The antibodies can facilitate the purification ofthe natural protein from cells and recombinantly produced proteinexpressed in host cells. In addition, such antibodies are useful todetect the presence of one of the proteins of the present invention incells or tissues to determine the pattern of expression of the proteinamong various tissues in an organism and over the course of normaldevelopment. Experimental data as provided in FIG. 1 indicates thatRas-like proteins of the present invention are expressed in humans ingerm cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, and brain, as indicated by virtual northern blot analysis. Inaddition, PCR-based tissue screening panels indicates expression inleukocytes. Further, such antibodies can be used to detect protein insitu, in vitro, or in a cell lysate or supernatant in order to evaluatethe abundance and pattern of expression. Also, such antibodies can beused to assess abnormal tissue distribution or abnormal expressionduring development. Antibody detection of circulating fragments of thefull-length protein can be used to identify turnover.

Further, the antibodies can be used to assess expression in diseasestates such as in active stages of the disease or in an individual witha predisposition toward disease related to the protein's function. Whena disorder is caused by an inappropriate tissue distribution,developmental expression, level of expression of the protein, orexpressed/processed form, the antibody can be prepared against thenormal protein. Experimental data as provided in FIG. 1 indicatesexpression in humans in germ cell tumors, retina, testis, liver/spleen,colon, melanotic melanoma, brain, and leukocytes. If a disorder ischaracterized by a specific mutation in the protein, antibodies specificfor this mutant protein can be used to assay for the presence of thespecific mutant protein.

The antibodies can also be used to assess normal and aberrantsubcellular localization of cells in the various tissues in an organism.Experimental data as provided in FIG. 1 indicates expression in humansin germ cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, brain, and leukocytes. The diagnostic uses can be applied, notonly in genetic testing, but also in monitoring a treatment modality.Accordingly, where treatment is ultimately aimed at correctingexpression level or the presence of aberrant sequence and aberranttissue distribution or developmental expression, antibodies directedagainst the or relevant fragments can be used to monitor therapeuticefficacy.

Additionally, antibodies are useful in pharmacogenomic analysis. Thus,antibodies prepared against polymorphic proteins can be used to identifyindividuals that require modified treatment modalities. The antibodiesare also useful as diagnostic tools as an immunological marker foraberrant protein analyzed by electrophoretic mobility, isoelectricpoint, tryptic peptide digest, and other physical assays known to thosein the art.

The antibodies are also useful for tissue typing. Experimental data asprovided in FIG. 1 indicates expression in humans in germ cell tumors,retina, testis, liver/spleen, colon, melanotic melanoma, brain, andleukocytes. Thus, where a specific protein has been correlated withexpression in a specific tissue, antibodies that are specific for thisprotein can be used to identify a tissue type.

The antibodies are also useful for inhibiting protein function, forexample, blocking the binding of the Ras-like protein to a bindingpartner such as a substrate. These uses can also be applied in atherapeutic context in which treatment involves inhibiting the protein'sfunction. An antibody can be used, for example, to block binding, thusmodulating (agonizing or antagonizing) the peptides activity. Antibodiescan be prepared against specific fragments containing sites required forfunction or against intact protein that is associated with a cell orcell membrane. See FIG. 2 for structural information relating to theproteins of the present invention.

The invention also encompasses kits for using antibodies to detect thepresence of a protein in a biological sample. The kit can compriseantibodies such as a labeled or labelable antibody and a compound oragent for detecting protein in a biological sample; means fordetermining the amount of protein in the sample; means for comparing theamount of protein in the sample with a standard; and instructions foruse.

Nucleic Acid Molecules

The present invention further provides isolated nucleic acid moleculesthat encode a Ras-like protein polypeptide of the present invention.Such nucleic acid molecules will consist of, consist essentially of, orcomprise a nucleotide sequence that encodes one of the Ras-like proteinpolypeptides of the present invention, an allelic variant thereof, or anortholog or paralog thereof.

As used herein, an “isolated” nucleic acid molecule is one that isseparated from other nucleic acid present in the natural source of thenucleic acid. Preferably, an “isolated” nucleic acid is free ofsequences which naturally flank the nucleic acid (i.e., sequenceslocated at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA ofthe organism from which the nucleic acid is derived. However, there canbe some flanking nucleotide sequences, for example up to about 5 KB,particularly contiguous peptide encoding sequences and peptide encodingsequences within the same gene but separated by introns in the genomicsequence. The important point is that the nucleic acid is isolated fromremote and unimportant flanking sequences such that it can be subjectedto the specific manipulations described herein such as recombinantexpression, preparation of probes and primers, and other uses specificto the nucleic acid sequences.

Moreover, an “isolated” nucleic acid molecule, such as a cDNA molecule,can be substantially free of other cellular material, or culture mediumwhen produced by recombinant techniques, or chemical precursors or otherchemicals when chemically synthesized. However, the nucleic acidmolecule can be fused to other coding or regulatory sequences and stillbe considered isolated.

For example, recombinant DNA molecules contained in a vector areconsidered isolated. Further examples of isolated DNA molecules includerecombinant DNA molecules maintained in heterologous host cells orpurified (partially or substantially) DNA molecules in solution.Isolated RNA molecules include in vivo or in vitro RNA transcripts ofthe isolated DNA molecules of the present invention. Isolated nucleicacid molecules according to the present invention further include suchmolecules produced synthetically.

Accordingly, the present invention provides nucleic acid molecules thatconsist of the nucleotide sequence shown in FIG. 1 or 3 (SEQ ID NO:1,transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleicacid molecule that encodes the protein provided in FIG. 2, SEQ ID NO:2.A nucleic acid molecule consists of a nucleotide sequence when thenucleotide sequence is the complete nucleotide sequence of the nucleicacid molecule. The present invention further provides nucleic acidmolecules that consist essentially of the nucleotide sequence shown inFIG. 1 or 3 (SEQ ID NO:1, transcript sequence and SEQ ID NO:3, genomicsequence), or any nucleic acid molecule that encodes the proteinprovided in FIG. 2, SEQ ID NO:2. A nucleic acid molecule consistsessentially of a nucleotide sequence when such a nucleotide sequence ispresent with only a few additional nucleic acid residues in the finalnucleic acid molecule.

The present invention further provides nucleic acid molecules thatcomprise the nucleotide sequences shown in FIG. 1 or 3 (SEQ ID NO:1,transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleicacid molecule that encodes the protein provided in FIG. 2, SEQ ID NO:2.A nucleic acid molecule comprises a nucleotide sequence when thenucleotide sequence is at least part of the final nucleotide sequence ofthe nucleic acid molecule. In such a fashion, the nucleic acid moleculecan be only the nucleotide sequence or have additional nucleic acidresidues, such as nucleic acid residues that are naturally associatedwith it or heterologous nucleotide sequences. Such a nucleic acidmolecule can have a few additional nucleotides or can comprises severalhundred or more additional nucleotides. A brief description of howvarious types of these nucleic acid molecules can be readilymade/isolated is provided below.

In FIGS. 1 and 3, both coding and non-coding sequences are provided.Because of the source of the present invention, humans genomic sequence(FIG. 3) and cDNA/transcript sequences (FIG. 1), the nucleic acidmolecules in the Figures will contain genomic intronic sequences, 5′ and3′ non-coding sequences, gene regulatory regions and non-codingintergenic sequences. In general such sequence features are either notedin FIGS. 1 and 3 or can readily be identified using computational toolsknown in the art. As discussed below, some of the non-coding regions,particularly gene regulatory elements such as promoters, are useful fora variety of purposes, e.g. control of heterologous gene expression,target for identifying gene activity modulating compounds, and areparticularly claimed as fragments of the genomic sequence providedherein.

Full-length genes may be cloned from known sequence using any one of anumber of methods known in the art. For example, a method which employsXL-PCR (Perkin-Elmer, Foster City, Calif.) to amplify long pieces of DNAmay be used. Other methods for obtaining full-length sequences are wellknown in the art.

The isolated nucleic acid molecules can encode the mature protein plusadditional amino or carboxyl-terminal amino acids, or amino acidsinterior to the mature peptide (when the mature form has more than onepeptide chain, for instance). Such sequences may play a role inprocessing of a protein from precursor to a mature form, facilitateprotein trafficking, prolong or shorten protein half-life, or facilitatemanipulation of a protein for assay or production, among other things.As generally is the case in situ, the additional amino acids may beprocessed away from the mature protein by cellular enzymes.

As mentioned above, the isolated nucleic acid molecules include, but arenot limited to, the sequence encoding the Ras-like protein polypeptidealone, the sequence encoding the mature peptide and additional codingsequences, such as a leader or secretory sequence (e.g., a pre-pro orpro-protein sequence), the sequence encoding the mature peptide, with orwithout the additional coding sequences, plus additional non-codingsequences, for example introns and non-coding 5′ and 3′ sequences suchas transcribed but non-translated sequences that play a role intranscription, mRNA processing (including splicing and polyadenylationsignals), ribosome binding, and stability of mRNA. In addition, thenucleic acid molecule may be fused to a marker sequence encoding, forexample, a peptide that facilitates purification.

Isolated nucleic acid molecules can be in the form of RNA, such as mRNA,or in the form of DNA, including cDNA and genomic DNA obtained bycloning or produced by chemical synthetic techniques or by a combinationthereof. The nucleic acid, especially DNA, can be double-stranded orsingle-stranded. Single-stranded nucleic acid can be the coding strand(sense strand) or the non-coding strand (anti-sense strand).

The invention further provides nucleic acid molecules that encodefragments of the peptides of the present invention and that encodeobvious variants of the Ras-like proteins of the present invention thatare described above. Such nucleic acid molecules may be naturallyoccurring, such as allelic variants (same locus), paralogs (differentlocus), and orthologs (different organism), or may be constructed byrecombinant DNA methods or by chemical synthesis. Such non-naturallyoccurring variants may be made by mutagenesis techniques, includingthose applied to nucleic acid molecules, cells, or whole organisms.Accordingly, as discussed above, the variants can contain nucleotidesubstitutions, deletions inversions, and/or insertions. Variation canoccur in either or both the coding and non-coding regions. Thevariations can produce both conservative and non-conservative amino acidsubstitutions.

The present invention further provides non-coding fragments of thenucleic acid molecules provided in the FIGS. 1 and 3. Preferrednon-coding fragments include, but are not limited to, promotersequences, enhancer sequences, gene modulating sequences, and genetermination sequences. Such fragments are useful in controllingheterologous gene expression and in developing screens to identifygene-modulating agents.

A fragment comprises a contiguous nucleotide sequence greater than 12 ormore nucleotides. Further, a fragment could be at least 30, 40, 50, 100250, or 500 nucleotides in length. The length of the fragment will bebased on its intended use. For example, the fragment can encodeepitope-bearing regions of the peptide, or can be useful as DNA probesand primers. Such fragments can be isolated using the known nucleotidesequence to synthesize an oligonucleotide probe. A labeled probe canthen be used to screen a cDNA library, genomic DNA library, or mRNA toisolate nucleic acid corresponding to the coding region. Further,primers can be used in PCR reactions to clone specific regions of gene.

A probe/primer typically comprises substantially a purifiedoligonucleotide or oligonucleotide pair. The oligonucleotide typicallycomprises a region of nucleotide sequence that hybridizes understringent conditions to at least about 12, 20, 25, 40, 50; or moreconsecutive nucleotides.

Orthologs, homologs, and allelic variants can be identified usingmethods well known in the art. As described in the Peptide Section,these variants-comprise a nucleotide sequence encoding a peptide that istypically 60-70%, 70-80%, 80-90%, and more typically at least about90-95% or more homologous to the nucleotide sequence shown in the Figuresheets or a fragment of this sequence. Such nucleic acid molecules canreadily be identified as being able to hybridize under moderate tostringent conditions, to the nucleotide sequence shown in the Figuresheets or a fragment of the sequence. The gene encoding the novel Rabprotein of the present invention is located on a genome component thathas been mapped to human chromosome 14 (as indicated in FIG. 3), whichis supported by multiple lines of evidence, such as STS and BAC mapdata.

As used herein, the term “hybridizes under stringent conditions” isintended to describe conditions for hybridization and washing underwhich nucleotide sequences encoding a peptide at least 60-70% homologousto each other typically remain hybridized to each other. The conditionscan be such that sequences at least about 60%, at least about 70%, or atleast about 80% or more homologous to each other typically remainhybridized to each other. Such stringent conditions are known to thoseskilled in the art and can be found in Current Protocols in MolecularBiology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. One example ofstringent hybridization conditions are hybridization in 6×sodiumchloride/sodium citrate (SSC) at about 45 C, followed by one or morewashes in 0.2×SSC, 0.1% SDS at 50-65° C. Examples of moderate to lowstringency hybridization conditions are well known in the art.

Nucleic Acid Molecule Uses

The nucleic acid molecules of the present invention are useful forprobes, primers, chemical intermediates, and in biological assays. Thenucleic acid molecules are useful as a hybridization probe for messengerRNA, transcript/cDNA and genomic DNA to isolate full-length cDNA andgenomic clones encoding the peptide described in FIG. 2 and to isolatecDNA and genomic clones that correspond to variants (alleles, orthologs,etc.) producing the same or related peptides shown in FIG. 2.

The probe can correspond to any sequence along the entire length of thenucleic acid molecules provided in the Figures. Accordingly, it could bederived from 5′ noncoding regions, the coding region, and 3′ noncodingregions. However, as discussed, fragments are not to be construed asthose, which may encompass fragments disclosed prior to the presentinvention.

The nucleic acid molecules are also useful as primers for PCR to amplifyany given region of a nucleic acid molecule and are useful to synthesizeantisense molecules of desired length and sequence.

The nucleic acid molecules are also useful for constructing recombinantvectors. Such vectors include expression vectors that express a portionof, or all of, the peptide sequences. Vectors also include insertionvectors, used to integrate into another nucleic acid molecule sequence,such as into the cellular genome, to alter in situ expression of a geneand/or gene product. For example, an endogenous coding sequence can bereplaced via homologous recombination with all or part of the codingregion containing one or more specifically introduced mutations.

The nucleic acid molecules are also useful for expressing antigenicportions of the proteins.

The nucleic acid molecules are also useful as probes for determining thechromosomal positions of the nucleic acid molecules by means of in situhybridization methods. The gene encoding the novel Rab protein of thepresent invention is located on a genome component that has been mappedto human chromosome 14 (as indicated in FIG. 3), which is supported bymultiple lines of evidence, such as STS and BAC map data.

The nucleic acid molecules are also useful in making vectors containingthe gene regulatory regions of the nucleic acid molecules of the presentinvention.

The nucleic acid molecules are also useful for designing ribozymescorresponding to all, or a part, of the mRNA produced from the nucleicacid molecules described herein.

The nucleic acid molecules are also useful for constructing host cellsexpressing a part, or all, of the nucleic acid molecules and peptides.Moreover, the nucleic acid molecules are useful for constructingtransgenic animals wherein a homolog of the nucleic acid molecule hasbeen “knocked-out” of the animal's genome.

The nucleic acid molecules are also useful for constructing transgenicanimals expressing all, or a part, of the nucleic acid molecules andpeptides.

The nucleic acid molecules are also useful for making vectors thatexpress part, or all, of the peptides.

The nucleic acid molecules are also useful as hybridization probes fordetermining the presence, level, form, and distribution of nucleic acidexpression. Experimental data as provided in FIG. 1 indicates thatRas-like proteins of the present invention are expressed in humans ingerm cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, and brain, as indicated by virtual northern blot analysis. Inaddition, PCR-based tissue screening panels indicates expression inleukocytes. Accordingly, the probes can be used to detect the presenceof, or to determine levels of, a specific nucleic acid molecule incells, tissues, and in organisms. The nucleic acid whose level isdetermined can be DNA or RNA. Accordingly, probes corresponding to thepeptides described herein can be used to assess expression and/or genecopy number in a given cell, tissue, or organism. These uses, arerelevant for diagnosis of disorders involving an increase or decrease inRas-like protein expression relative to normal results.

In vitro techniques for detection of mRNA include Northernhybridizations and in situ hybridizations. In vitro techniques fordetecting DNA include Southern hybridizations and in situ hybridization.

Probes can be used as a part of a diagnostic test kit for identifyingcells or tissues that express a Ras-like protein, such as by measuring alevel of a receptor-encoding nucleic acid in a sample of cells from asubject e.g., mRNA or genomic DNA, or determining if a receptor gene hasbeen mutated. Experimental data as provided in FIG. 1 indicates thatRas-like proteins of the present invention are expressed in humans ingerm cell tumors, retina, testis, liver/spleen, colon, melanoticmelanoma, and brain, as indicated by virtu northern blot analysis. Inaddition, PCR-based tissue screening panels indicates expression inleukocytes.

Nucleic acid expression assays are useful for drug screening to identifycompounds that modulate Ras-like protein nucleic acid expression.

The invention thus provides a method for identifying a compound that canbe used to treat a disorder associated with nucleic acid expression ofthe Ras-like protein gene, particularly biological and pathologicalprocesses that are mediated by the Ras-like protein in cells and tissuesthat express it. Experimental data as provided in FIG. 1 indicatesexpression in humans in germ cell tumors, retina, testis, liver/spleen,colon, melanotic melanoma, brain, and leukocytes. The method typicallyincludes assaying the ability of the compound to modulate the expressionof the Ras-like protein nucleic acid and thus identifying a compoundthat can be used to treat a disorder characterized by undesired Ras-likeprotein nucleic acid expression. The assays can be performed incell-based and cell-free systems. Cell-based assays include cellsnaturally expressing the Ras-like protein nucleic acid or recombinantcells genetically engineered to express specific nucleic acid sequences.

The assay for Ras-like protein nucleic acid expression can involvedirect assay of nucleic acid levels, such as mRNA levels, or oncollateral compounds involved in the signal pathway. Further, theexpression of genes that are up- or down-regulated in response to theRas-like protein signal pathway can also be assayed. In this embodimentthe regulatory regions of these genes can be operably linked to areporter gene such as luciferase.

Thus, modulators of Ras-like protein gene expression can be identifiedin a method wherein a cell is contacted with a candidate compound andthe expression of mRNA determined. The level of expression of Ras-likeprotein mRNA in the presence of the candidate compound is compared tothe level of expression of Ras-like protein mRNA in the absence of thecandidate compound. The candidate compound can then be identified as amodulator of nucleic acid expression based on this comparison and beused, for example to treat a disorder characterized by aberrant nucleicacid expression. When expression of mRNA is statistically significantlygreater in the presence of the candidate compound than in its absence,the candidate compound is identified as a stimulator of nucleic acidexpression. When nucleic acid expression is statistically significantlyless in the presence of the candidate compound than in its absence, thecandidate compound is identified as an inhibitor of nucleic acidexpression.

The invention further provides methods of treatment, with the nucleicacid as a target, using a compound identified through drug screening asa gene modulator to modulate Ras-like protein nucleic acid expression incells and tissues that express the Ras-like protein. Experimental dataas provided in FIG. 1 indicates that Ras-like proteins of the presentinvention are expressed in humans in germ cell tumors, retina, testis,liver/spleen, colon, melanotic melanoma, and brain, as indicated byvirtual northern blot analysis. In addition, PCR-based tissue screeningpanels indicates expression in leukocytes. Modulation includes bothup-regulation (i.e. activation or agonization) or down-regulation(suppression or antagonization) of nucleic acid expression.

Alternatively, a modulator for Ras-like protein nucleic acid expressioncan be a small molecule or drug identified using the screening assaysdescribed herein as long as the drug or small molecule inhibits theRas-like protein nucleic acid expression in the cells and tissues thatexpress the protein. Experimental data as provided in FIG. 1 indicatesexpression in humans in germ cell tumors, retina, testis, liver/spleen,colon, melanotic melanoma, brain, and leukocytes.

The nucleic acid molecules are also useful for monitoring theeffectiveness of modulating compounds on the expression or activity ofthe Ras-like protein gene in clinical trials or in a treatment regimen.Thus, the gene expression pattern can serve as a barometer for thecontinuing effectiveness of treatment with the compound, particularlywith compounds to which a patient can develop resistance. The geneexpression pattern can also serve as a marker indicative of aphysiological response of the affected cells to the compound.Accordingly, such monitoring would allow either increased administrationof the compound or the administration of alternative compounds to whichthe patient has not become resistant. Similarly, if the level of nucleicacid expression falls below a desirable level, administration of thecompound could be commensurately decreased.

The nucleic acid molecules are also useful in diagnostic assays forqualitative changes in Ras-like protein nucleic acid, and particularlyin qualitative changes that lead to pathology. The nucleic acidmolecules can be used to detect mutations in Ras-like protein genes andgene expression products such as mRNA. The nucleic acid molecules can beused as hybridization probes to detect naturally occurring geneticmutations in the Ras-like protein gene and thereby to determine whethera subject with the mutation is at risk for a disorder caused by themutation. Mutations include deletion, addition, or substitution of oneor more nucleotides in the gene, chromosomal rearrangement, such asinversion or transposition, modification of genomic DNA, such asaberrant methylation patterns, or changes in gene copy number, such asamplification. Detection of a mutated form of the Ras-like protein geneassociated with a dysfunction provides a diagnostic tool for an activedisease or susceptibility to disease when the disease results fromoverexpression, underexpression, or altered expression of a Ras-likeprotein.

Individuals carrying mutations in the Ras-like protein gene can bedetected at the nucleic acid level by a variety of techniques. The geneencoding the novel Rab protein of the present invention is located on agenome component that has been mapped to human chromosome 14 (asindicated in FIG. 3), which is supported by multiple lines of evidence,such as STS and BAC map data. Genomic DNA can be analyzed directly orcan be amplified by using PCR prior to analysis. RNA or cDNA can be usedin the same way. In some uses, detection of the mutation involves theuse of a probe/primer in a polymerase chain reaction (PCR) (see, e.g.U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR,or, alternatively, in a ligation chain reaction (LCR) (see, e.g.,Landegran et al., Science 241:1077-1080 (1988); and Nakazawa et al.,PNAS 91:360-364 (1994)), the latter of which can be particularly usefulfor detecting point mutations in the gene (see Abravaya et al., NucleicAcids Res. 23:675-682 (1995)). This method can include the steps ofcollecting a sample of cells from a patient, isolating nucleic acid(e.g., genomic, mRNA or both) from the cells of the sample, contactingthe nucleic acid sample with one or more primers which specificallyhybridize to a gene under conditions such that hybridization andamplification of the gene (if present) occurs, and detecting thepresence or absence of an amplification product, or detecting the sizeof the amplification product and comparing the length to a controlsample. Deletions and insertions can be detected by a change in size ofthe amplified product compared to the normal genotype. Point mutationscan be identified by hybridizing amplified DNA to normal RNA orantisense DNA sequences.

Alternatively, mutations in a Ras-like protein gene can be directlyidentified, for example, by alterations in restriction enzyme digestionpatterns determined by gel electrophoresis.

Further, sequence-specific ribozymes (U.S. Pat. No. 5,498,531) can beused to score for the presence of specific mutations by development orloss of a ribozyme cleavage site. Perfectly matched sequences can bedistinguished from mismatched sequences by nuclease cleavage digestionassays or by differences in melting temperature.

Sequence changes at specific locations can also be assessed by nucleaseprotection assays such as RNase and S1 protection or the chemicalcleavage method. Furthermore, sequence differences between a mutantRas-like protein gene and a wild-type gene can be determined by directDNA sequencing. A variety of automated sequencing procedures can beutilized when performing the diagnostic assays (Naeve, C. W.,Biotechniques 19:448 (1995)), including sequencing by mass spectrometry(see, e.g., PCT International Publication No. WO 94/16101; Cohen et al.,Adv. Chromatogr. 36:127-162 (1996); and Griffin et al., Appl. Biochem.Biotechnol. 38:147-159 (1993)).

Other methods for detecting mutations in the gene include methods inwhich protection from cleavage agents is used to detect mismatched basesin RNA/RNA or RNA/DNA duplexes (Myers et al., Science 230:1242 (1985));Cotton et al., PNAS 85:4397 (1988); Saleeba et al., Meth. Enzymol.217:286-295 (1992)), electrophoretic mobility of mutant and wild typenucleic acid is compared (Orita et al., PNAS 86:2766 (1989); Cotton etal., Mutat. Res. 285:125-144 (1993); and Hayashi et al., Genet. Anal.Tech. Appl. 9:73-79 (1992)), and movement of mutant or wild-typefragments in polyacrylamide gels containing a gradient of denaturant isassayed using denaturing gradient gel electrophoresis (Myers et al.,Nature 313:495 (1985)). Examples of other techniques for detecting pointmutations include, selective oligonucleotide hybridization, selectiveamplification, and selective primer extension.

The nucleic acid molecules are also useful for testing an individual fora genotype that while not necessarily causing the disease, neverthelessaffects the treatment modality. Thus, the nucleic acid molecules can beused to study the relationship between an individual's genotype and theindividual's response to a compound used for treatment pharmacogenomicrelationship). Accordingly, the nucleic acid molecules described hereincan be used to assess the mutation content of the Ras-like protein genein an individual in order to select an appropriate compound or dosageregimen for treatment.

Thus nucleic acid molecules displaying genetic variations that affecttreatment provide a diagnostic target that can be used to tailortreatment in an individual. Accordingly, the production of recombinantcells and animals containing these polymorphisms allow effectiveclinical design of treatment compounds and dosage regimens.

The nucleic acid molecules are thus useful as antisense constructs tocontrol Ras-like protein gene expression in cells, tissues, andorganisms. A DNA antisense nucleic acid molecule is designed to becomplementary to a region of the gene involved in transcription,preventing transcription and hence production of Ras-like protein. Anantisense RNA or DNA nucleic acid molecule would hybridize to the mRNAand thus block translation of mRNA into Ras-like protein.

Alternatively, a class of antisense molecules can be used to inactivatemRNA in order to decrease expression of Ras-like protein nucleic acid.Accordingly, these molecules can treat a disorder characterized byabnormal or undesired Ras-like protein nucleic acid expression. Thistechnique involves cleavage by means of ribozymes containing nucleotidesequences complementary to one or more regions in the mRNA thatattenuate the ability of the mRNA to be translated. Possible regionsinclude coding regions and particularly coding regions corresponding tothe catalytic and other functional activities of the Ras-like protein,such as ligand binding.

The nucleic acid molecules also provide vectors for gene therapy inpatients containing cells that are aberrant in Ras-like protein geneexpression. Thus, recombinant cells, which include the patient's cellsthat have been engineered ex vivo and returned to the patient, areintroduced into an individual where the cells produce the desiredRas-like protein to treat the individual.

The invention also encompasses kits for detecting the presence of aRas-like protein nucleic acid in a biological sample. Experimental dataas provided in FIG. 1 indicates that Ras-like proteins of the presentinvention are expressed in humans in germ cell tumors, retina, testis,liver/spleen, colon, melanotic melanoma, and brain, as indicated byvirtual northern blot analysis. In addition, PCR-based tissue screeningpanels indicates expression in leukocytes. For example, the kit cancomprise reagents such as a labeled or labelable nucleic acid or agentcapable of detecting Ras-like protein nucleic acid in a biologicalsample; means for determining the amount of Ras-like protein nucleicacid in the sample; and means for comparing the amount of Ras-likeprotein nucleic acid in the sample with a standard. The compound oragent can be packaged in a suitable container. The kit can furthercomprise instructions for using the kit to detect Ras-like protein mRNAor DNA.

Nucleic Acid Arrays

The present invention further provides arrays or microarrays of nucleicacid molecules that are based on the sequence information provided inFIGS. 1 and 3 (SEQ ID NOS:1 and 3).

As used herein “Arrays” or “Microarrays” refers to an array of distinctpolynucleotides or oligonucleotides synthesized on a substrate, such aspaper, nylon or other type of membrane, filter, chip, glass slide, orany other suitable solid support. In one embodiment, the microarray isprepared and used according to the methods described in U.S. Pat. No.5,837,832, Chee et al., PCT application W095/11995 (Chee et al.),Lockhart, D. J. et al. (1996; Nat. Biotech. 14: 1675-1680) and Schena,M. et al. (1996; Proc. Natl. Acad. Sci. 93: 10614-10619), all of whichare incorporated herein in their entirety by reference. In otherembodiments, such arrays are produced by the methods described by Brownet. al., U.S. Pat. No. 5,807,522.

The microarray is preferably composed of a large number of unique,single-stranded nucleic acid sequences, usually either syntheticantisense oligonucleotides or fragments of cDNAs, fixed to a solidsupport. The oligonucleotides are preferably about 6-60 nucleotides inlength, more preferably 15-30 nucleotides in length, and most preferablyabout 20-25 nucleotides in length. For a certain type of microarray, itmay be preferable to use oligonucleotides that are only 7-20 nucleotidesin length. The microarray may contain oligonucleotides that cover theknown 5′, or 3′, sequence, sequential oligonucleotides that cover thefull-length sequence; or unique oligonucleotides selected fromparticular areas along the length of the sequence. Polynucleotides usedin the microarray may be oligonucleotides that are specific to a gene orgenes of interest.

In order to produce oligonucleotides to a known sequence for amicroarray, the gene(s) of interest (or an ORF identified from thecontigs of the present invention) is typically examined using a computeralgorithm that starts at the 5′ or at the 3′ end of the nucleotidesequence. Typical algorithms will then identify oligomers of definedlength that are unique to the gene, have a GC content within a rangesuitable for hybridization, and lack predicted secondary structure thatmay interfere with hybridization. In certain situations it may beappropriate to use pairs of oligonucleotides on a microarray. The“pairs” will be identical, except for one nucleotide that preferably islocated in the center of the sequence. The second oligonucleotide in thepair (mismatched by one) serves as a control. The number ofoligonucleotide pairs may range from two to one million. The oligomersare synthesized at designated areas on a substrate using alight-directed chemical process. The substrate may be paper, nylon orother type of membrane, filter, chip, glass slide or any other suitablesolid support.

In another aspect, an oligonucleotide may be synthesized on the surfaceof the substrate by using a chemical coupling procedure and an ink jetapplication apparatus, as described in PCT application W095/251116(Baldeschweiler et al.) which is incorporated herein in its entirety byreference. In another aspect, a “gridded” array analogous to a dot (orslot) blot may be used to arrange and link cDNA fragments oroligonucleotides to the surface of a substrate using a vacuum system,thermal, UV, mechanical or chemical bonding procedures. An array, suchas those described above, may be produced by hand or by using availabledevices (slot blot or dot blot apparatus), materials (any suitable solidsupport), and machines (including robotic instruments), and may contain8, 24, 96, 384, 1536, 6144 or more oligonucleotides, or any other numberbetween two and one million which lends itself to the efficient use ofcommercially available instrumentation.

In order to conduct sample analysis using a microarray, the RNA or DNAfrom a biological sample is made into hybridization probes. The mRNA isisolated, and cDNA is produced and used as a template to make antisenseRNA (aRNA). The aRNA is amplified in the presence of fluorescentnucleotides, and labeled probes are incubated with the microarray sothat the probe sequences hybridize to complementary oligonucleotides ofthe microarray. Incubation conditions are adjusted so that hybridizationoccurs with precise complementary matches or with various degrees ofless complementarity. After removal of nonhybridized probes, a scanneris used to determine the levels and patterns of fluorescence. Thescanned images are examined to determine degree of complementarity andthe relative abundance of each oligonucleotide sequence on themicroarray. The biological samples may be obtained from any bodilyfluids (such as blood, urine, saliva, phlegm, gastric juices, etc.),cultured cells, biopsies, or other tissue preparations. A detectionsystem may be used to measure the absence, presence, and amount ofhybridization for all of the distinct sequences simultaneously. Thisdata may be used for large-scale correlation studies on the sequences,expression patterns, mutations, variants, or polymorphisms amongsamples.

Using such arrays, the present invention provides methods to identifythe expression of one or more of the proteins/peptides of the presentinvention. In detail, such methods comprise incubating a test samplewith one or more nucleic acid molecules and assaying for binding of thenucleic acid molecule with components within the test sample. Suchassays will typically involve arrays comprising many genes, at least oneof which is a gene of the present invention.

Conditions for incubating a nucleic acid molecule with a test samplevary. Incubation conditions depend on the format employed in the assay,the detection methods employed, and the type and nature of the nucleicacid molecule used in the assay. One skilled in the art will recognizethat any one of the commonly available hybridization, amplification orarray assay formats can readily be adapted to employ the novel fragmentsof the human genome disclosed herein. Examples of such assays can befound in Chard, T, An Introduction to Radioimmunoassay and RelatedTechniques, Elsevier Science Publishers, Amsterdam, The Netherlands(1986); Bullock, G. R. et al., Techniques in Immunocytochemistry,Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3(1985); Tijssen, P., Practice and Theory of Enzyme Immunoassays:Laboratory Techniques in Biochemistry and Molecular Biology, ElsevierScience Publishers, Amsterdam, The Netherlands (1985).

The test samples of the present invention include cells, protein ormembrane extracts of cells. The test sample used in the above-describedmethod will vary based on the assay format, nature of the detectionmethod and the tissues, cells or extracts used as the sample to beassayed. Methods for preparing nucleic acid extracts or of cells arewell known in the art and can be readily be adapted in order to obtain asample that is compatible with the system utilized.

In another embodiment of the present invention, kits are provided whichcontain the necessary reagents to carry out the assays of the presentinvention.

Specifically, the invention provides a compartmentalized kit to receive,in close confinement, one or more containers which comprises: (a) afirst container comprising one of the nucleic acid molecules that canbind to a fragment of the human genome disclosed herein; and (b) one ormore other containers comprising one or more of the following: washreagents, reagents capable of detecting presence of a bound nucleicacid. Preferred kits will include chips that are capable of detectingthe expression of 10 or more, 100 or more, or 500 or more, 1000 or more,or all of the genes expressed in Human.

In detail, a compartmentalized kit includes any kit in which reagentsare contained in separate containers. Such containers include smallglass containers, plastic containers, strips of plastic, glass or paper,or arraying material such as silica. Such containers allows one toefficiently transfer reagents from one compartment to anothercompartment such that the samples and reagents are notcross-contaminated, and the agents or solutions of each container can beadded in a quantitative fashion from one compartment to another. Suchcontainers will include a container which will accept the test sample, acontainer which contains the nucleic acid probe, containers whichcontain wash reagents (such as phosphate buffered saline, Tris-buffers,etc.), and containers which contain the reagents used to detect thebound probe. One skilled in the art will readily recognize that thepreviously unidentified Ras-like protein genes of the present inventioncan be routinely identified using the sequence information disclosedherein can be readily incorporated into one of the established kitformats which are well known in the art, particularly expression arrays.

Vectors/Host Cells

The invention also provides vectors containing the nucleic acidmolecules described herein. The term “vector” refers to a vehicle,preferably a nucleic acid molecule, which can transport the nucleic acidmolecules. When the vector is a nucleic acid molecule, the nucleic acidmolecules are covalently linked to the vector nucleic acid. With thisaspect of the invention, the vector includes a plasmid, single or doublestranded phage, a single or double stranded RNA or DNA viral vector, orartificial chromosome, such as a BAC, PAC, YAC, OR MAC.

A vector can be maintained in the host cell as an extrachromosomalelement where it replicates and produces additional copies of thenucleic acid molecules. Alternatively, the vector may integrate into thehost cell genome and produce additional copies of the nucleic acidmolecules when the host cell replicates.

The invention provides vectors for the maintenance (cloning vectors) orvectors for expression (expression vectors) of the nucleic acidmolecules. The vectors can function in procaryotic or eukaryotic cellsor in both (shuttle vectors).

Expression vectors contain cis-acting regulatory regions that areoperably linked in the vector to the nucleic acid molecules such thattranscription of the nucleic acid molecules is allowed in a host cell.The nucleic acid molecules can be introduced into the host cell with aseparate nucleic acid molecule capable of affecting transcription. Thus,the second nucleic acid molecule may provide a trans-acting factorinteracting with the cis-regulatory control region to allowtranscription of the nucleic acid molecules from the vector.Alternatively, a trans-acting factor may be supplied by the host cell.Finally, a trans-acting factor can be produced from the vector itself.It is understood, however, that in some embodiments, transcriptionand/or translation of the nucleic acid molecules can occur in acell-free system.

The regulatory sequence to which the nucleic acid molecules describedherein can be operably linked include promoters for directing mRNAtranscription. These include, but are not limited to, the left promoterfrom bacteriophage λ, the lac, TRP, and TAC promoters from E. coli, theearly and late promoters from SV40, the CMV immediate early promoter,the adenovirus early and late promoters, and retrovirus long-terminalrepeats.

In addition to control regions that promote transcription, expressionvectors may also include regions that modulate transcription, such asrepressor binding sites and enhancers. Examples include the SV40enhancer, the cytomegalovirus immediate early enhancer, polyomaenhancer, adenovirus enhancers, and retrovirus LTR enhancers.

In addition to containing sites for transcription initiation andcontrol, expression vectors can also contain sequences necessary fortranscription termination and, in the transcribed region a ribosomebinding site for translation. Other regulatory control elements forexpression include initiation and termination codons as well aspolyadenylation signals. The person of ordinary skill in the art wouldbe aware of the numerous regulatory sequences that are useful inexpression vectors. Such regulatory sequences are described, forexample, in Sambrook et al., Molecular Cloning: A Laboratory Manual. 2nded., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,(1989).

A variety of expression vectors can be used to express a nucleic acidmolecule. Such vectors include chromosomal, episomal, and virus-derivedvectors, for example vectors derived from bacterial plasmids, frombacteriophage, from yeast episomes, from yeast chromosomal elements,including yeast artificial chromosomes, from viruses such asbaculoviruses, papovaviruses such as SV40, Vaccinia viruses,adenoviruses, poxviruses, pseudorabies viruses, and retroviruses.Vectors may also be derived from combinations of these sources such asthose derived from plasmid and bacteriophage genetic elements, e.g.cosmids and phagemids. Appropriate cloning and expression vectors forprokaryotic and eukaryotic hosts are described in Sambrook et al.,Molecular Cloning: A Laboratory Manual. 2nd ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., (1989).

The regulatory sequence may provide constitutive expression in one ormore host cells (i.e. tissue specific) or may provide for inducibleexpression in one or more cell types such as by temperature, nutrientadditive, or exogenous factor such as a hormone or other ligand. Avariety of vectors providing for constitutive and inducible expressionin prokaryotic and eukaryotic hosts are well known to those of ordinaryskill in the art.

The nucleic acid molecules can be inserted into the vector nucleic acidby well-known methodology. Generally, the DNA sequence that willultimately be expressed is joined to an expression vector by cleavingthe DNA sequence and the expression vector with one or more restrictionenzymes and then ligating the fragments together. Procedures forrestriction enzyme digestion and ligation are well known to those ofordinary skill in the art.

The vector containing the appropriate nucleic acid molecule can beintroduced into an appropriate host cell for propagation or expressionusing well-known techniques. Bacterial cells include, but are notlimited to, E. coli, Streptomyces, and Salmonella typhimurium.Eukaryotic cells include, but are not limited to, yeast, insect cellssuch as Drosophila, animal cells such as COS and CHO cells, and plantcells.

As described herein, it may be desirable to express the peptide as afusion protein. Accordingly, the invention provides fusion vectors thatallow for the production of the peptides. Fusion vectors can increasethe expression of a recombinant protein, increase the solubility of therecombinant protein, and aid in the purification of the protein byacting for example as a ligand for affinity purification. A proteolyticcleavage site may be introduced at the junction of the fusion moiety sothat the desired peptide can ultimately be separated from the fusionmoiety. Proteolytic enzymes include, but are not limited to, factor Xa,thrombin, and enteroRas-like protein. Typical fusion expression vectorsinclude pGEX (Smith et al., Gene 67:31-40 (1988)), pMAL (New EnglandBiolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) whichfuse glutathione S-transferase (GST), maltose E binding protein, orprotein A, respectively, to the target recombinant protein. Examples ofsuitable inducible non-fusion E. coli expression vectors include pTrc(Amann et al., Gene 69:301-315 (1988)) and pET 11d (Studier et al., GeneExpression Technology: Methods in Enzymology 185:60-89 (1990)).

Recombinant protein expression can be maximized in a host bacteria byproviding a genetic background wherein the host cell has an impairedcapacity to proteolytically cleave the recombinant protein. (Gottesman,S., Gene Expression Technology: Methods in Enzymology 185, AcademicPress, San Diego, Calif. (1990)119-128). Alternatively, the sequence ofthe nucleic acid molecule of interest can be altered to providepreferential codon usage for a specific host cell, for example E. coli.(Wada et al., Nucleic Acids Res. 20:2111-2118 (1992)).

The nucleic acid molecules can also be expressed by expression vectorsthat are operative in yeast. Examples of vectors for expression in yeaste.g., S. cerevisiae include pYepSecI (Baldari, et al., EMBO J. 6:229-234(1987)), pMFa (Kurjan et al., Cell 30:933-943(1982)), pJRY88 (Schultz etal., Gene 54:113-123 (1987)), and pYES2 (Invitrogen Corporation, SanDiego, Calif.).

The nucleic acid molecules can also be expressed in insect cells using,for example, baculovirus expression vectors. Baculovirus vectorsavailable for expression of proteins in cultured insect cells (e.g., Sf9cells) include the pAc series (Smith et al., Mol. Cell Biol. 3:2156-2165(1983)) and the pVL series (Lucklow et al., Virology 170:31-39 (1989)).

In certain embodiments of the invention, the nucleic acid moleculesdescribed herein are expressed in mammalian cells using mammalianexpression vectors. Examples of mammalian expression vectors includepCDM8 (Seed, B. Nature 329:840(1987)) and pMT2PC (Kaufman et al., EMBOJ. 6:187-195 (1987)).

The expression vectors listed herein are provided by way of example onlyof the well-known vectors available to those of ordinary skill in theart that would be useful to express the nucleic acid molecules. Theperson of ordinary skill in the art would be aware of other vectorssuitable for maintenance, propagation, or expression of the nucleic acidmolecules described herein. These are found for example in Sambrook, J.,Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual.2nd ed, Cold Spring Harbor Laboratory, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1989.

The invention also encompasses vectors in which the nucleic acidsequences described herein are cloned into the vector in reverseorientation, but operably linked to a regulatory sequence that permitstranscription of antisense RNA. Thus, an antisense transcript can beproduced to all, or to a portion, of the nucleic acid molecule sequencesdescribed herein, including both coding and non-coding regions.Expression of this antisense RNA is subject to each of the parametersdescribed above in relation to expression of the sense RNA (regulatorysequences, constitutive or inducible expression, tissue-specificexpression).

The invention also relates to recombinant host cells containing thevectors described herein. Host cells therefore include prokaryoticcells, lower eukaryotic cells such as yeast, other eukaryotic cells suchas insect cells, and higher eukaryotic cells such as mammalian cells.

The recombinant host cells are prepared by introducing the vectorconstructs described herein into the cells by techniques readilyavailable to the person of ordinary skill in the art. These include, butare not limited to, calcium phosphate transfection,DEAE-dextran-mediated transfection, cationic lipid-mediatedtransfection, electroporation, transduction, infection, lipofection, andother techniques such as those found in Sambrook, et al. (MolecularCloning: A Laboratory Manual, 2nd, ed, Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).

Host cells can contain more than one vector. Thus, different nucleotidesequences can be introduced on different vectors of the same cell.Similarly, the nucleic acid molecules can be introduced either alone orwith other nucleic acid molecules that are not related to the nucleicacid molecules such as those providing trans-acting factors forexpression vectors. When more than one vector is introduced into a cell,the vectors can be introduced independently, co-introduced, or joined tothe nucleic acid molecule vector.

In the case of bacteriophage and viral vectors, these can be introducedinto cells as packaged or encapsulated virus by standard procedures forinfection and transduction. Viral vectors can be replication-competentor replication-defective; In the case in which viral replication isdefective, replication will occur in host cells providing functions thatcomplement the defects.

Vectors generally include selectable markers that enable the selectionof the subpopulation of cells that contain the recombinant vectorconstructs. The marker can be contained in the same vector that containsthe nucleic acid molecules described herein or may be on a separatevector. Markers include tetracycline or ampicillin-resistance genes forprokaryotic host cells and dihydrofolate reductase or neomycinresistance for eukaryotic host cells. However, any marker that providesselection for a phenotypic trait will be effective.

While the mature proteins can be produced in bacteria, yeast, mammaliancells, and other cells under the control of the appropriate regulatorysequences, cell-free transcription and translation systems can also beused to produce these proteins using RNA derived from the DNA constructsdescribed herein.

Where secretion of the peptide is desired, which is difficult to achievewith multi-transmembrane domain containing proteins such as kinases,appropriate secretion signals are incorporated into the vector. Thesignal sequence can be endogenous to the peptides or heterologous tothese peptides.

Where the peptide is not secreted into the medium, which is typicallythe case with kinases, the protein can be isolated from the host cell bystandard disruption procedures, including freeze thaw; sonication,mechanical disruption, use of lysing agents and the like. The peptidecan then be recovered and purified by well-known purification methodsincluding ammonium sulfate precipitation, acid extraction, anion orcationic exchange chromatography, phosphocellulose chromatography,hydrophobic-interaction chromatography, affinity chromatography,hydroxylapatite chromatography, lectin chromatography, or highperformance liquid chromatography.

It is also understood that depending upon the host cell in recombinantproduction of the peptides described herein, the peptides can havevarious glycosylation patterns, depending upon the cell, or maybenon-glycosylated as when produced in bacteria. In addition, the peptidesmay include an initial modified methionine in some cases as a result ofa host-mediated process.

Uses of Vectors and Host Cells

The recombinant host cells expressing the peptides described herein havea variety of uses. First, the cells are useful for producing a Ras-likeprotein polypeptide that can be further purified to produce desiredamounts of Ras-like protein or fragments. Thus, host cells containingexpression vectors are useful for peptide production.

Host cells are also useful for conducting cell-based assays involvingthe Ras-like protein or Ras-like protein fragments. Thus, a recombinanthost cell expressing a native Ras-like protein is useful for assayingcompounds that stimulate or inhibit Ras-like protein function.

Host cells are also useful for identifying Ras-like protein mutants inwhich these functions are affected. If the mutants naturally occur andgive rise to a pathology, host cells containing the mutations are usefulto assay compounds that have a desired effect on the mutant Ras-likeprotein (for example, stimulating or inhibiting function) which may notbe indicated by their effect on the native Ras-like protein.

Genetically engineered host cells can be further used to producenon-human transgenic animals. A transgenic animal is preferably amammal, for example a rodent, such as a rat or mouse, in which one ormore of the cells of the animal include a transgene. A transgene isexogenous DNA which is integrated into the genome of a cell from which atransgenic animal develops and which remains in the genome of the matureanimal in one or more cell types or tissues of the transgenic animal.These animals are useful for studying the function of a Ras-like proteinand identifying and evaluating modulators of Ras-like protein activity.Other examples of transgenic animals include non-human primates, sheep,dogs, cows, goats, chickens, and amphibians.

A transgenic animal can be produced by introducing nucleic acid into themale pronuclei of a fertilized oocyte, e.g., by microinjection,retroviral infection, and allowing the oocyte to develop in apseudopregnant female foster animal. Any of the Ras-like proteinnucleotide sequences can be introduced as a transgene into the genome ofa non-human animal, such as a mouse.

Any of the regulatory or other sequences useful in expression vectorscan form part of the transgenic sequence. This includes intronicsequences and polyadenylation signals, if not already included. Atissue-specific regulatory sequence(s) can be operably linked to thetransgene to direct expression of the Ras-like protein to particularcells.

Methods for generating transgenic animals via embryo manipulation andmicroinjection, particularly animals such as mice, have becomeconventional in the art and are described, for example, in U.S. Pat.Nos. 4,736,866 and 4,870,009, both by Leder et al., U.S. Pat. No.4,873,191 by Wagner et al. and in Hogan, B., Manipulating the MouseEmbryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1986). Similar methods are used for production of other transgenicanimals. A transgenic founder animal can be identified based upon thepresence of the transgene in its genome and/or expression of transgenicmRNA in tissues or cells of the animals. A transgenic founder animal canthen be used to breed additional animals carrying the transgene.Moreover, transgenic animals carrying a transgene can further be bred toother transgenic animals carrying other transgenes. A transgenic animalalso includes animals in which the entire animal or tissues in theanimal have been produced using the homologously recombinant host cellsdescribed herein.

In another embodiment, transgenic non-human animals can be producedwhich contain selected systems which allow for regulated expression ofthe transgene. One example of such a system is the cre/loxP recombinasesystem of bacteriophage P1. For a description of the cre/loxPrecombinase system, see, e.g., Lakso et al. PNAS 89:6232-6236 (1992).Another example of a recombinase system is the FLP recombinase system ofS. cerevisiae (O'Gorman et al. Science 251:1351-1355 (1991). If acre/loxP recombinase system is used to regulate expression of thetransgene, animals containing transgenes encoding both the Crerecombinase and a selected protein is required. Such animals can beprovided through the construction of “double” transgenic animals, e.g.,by mating two transgenic animals, one containing a transgene encoding aselected protein and the other containing a transgene encoding arecombinase.

Clones of the non-human transgenic animals described herein can also beproduced according to the methods described in Wilmut, I. et al. Nature385:810-813 (1997) and PCT International Publication Nos. WO 97/07668and WO 97/07669. In brief, a cell, e.g., a somatic cell, from thetransgenic animal can be isolated and induced to exit the growth cycleand enter G_(o) phase. The quiescent cell can then be fused, e.g.,through the use of electrical pulses, to an enucleated oocyte from ananimal of the same species from which the quiescent cell is isolated.The reconstructed oocyte is then cultured such that it develops tomorula or blastocyst and then transferred to pseudopregnant femalefoster animal. The offspring born of this female foster animal will be aclone of the animal from which the cell, e.g., the somatic cell, isisolated.

Transgenic animals containing recombinant cells that express thepeptides described herein are useful to conduct the assays describedherein in an in vivo context. Accordingly, the various physiologicalfactors that are present in vivo and that could effect ligand binding,Ras-like protein activation, and signal transduction, may not be evidentfrom in vitro cell-free or cell-based assays. Accordingly, it is usefulto provide non-human transgenic animals to assay in vivo Ras-likeprotein function, including ligand interaction, the effect of specificmutant Ras-like proteins on Ras-like protein function and ligandinteraction, and the effect of chimeric Ras-like proteins. It is alsopossible to assess the effect of null mutations, which is mutations thatsubstantially or completely eliminate one or more Ras-like proteinfunctions.

All publications and patents mentioned in the above specification areherein incorporated by reference. Various modifications and variationsof the described method and system of the invention will be apparent tothose skilled in the art without departing from the scope and spirit ofthe invention. Although the invention has been described in connectionwith specific preferred embodiments, it should be understood that theinvention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications of the above-described modesfor carrying out the invention, which are obvious to those skilled inthe field of molecular biology or related fields, are intended to bewithin the scope of the following claims.

1. An isolated polypeptide consisting of an amino acid sequence selectedfrom the group consisting of: (a) an amino acid sequence shown in SEQ IDNO:2; (b) an amino acid sequence of an allelic variant of an amino acidsequence shown in SEQ ID NO:2, wherein said allelic variant is encodedby a nucleic acid molecule that hybridizes under stringent conditions tothe opposite strand of a nucleic acid molecule shown in SEQ ID NOS:1 or3; (c) an amino acid sequence of an ortholog of an amino acid sequenceshown in SEQ ID NO:2, wherein said ortholog is encoded by a nucleic acidmolecule that hybridizes under stringent conditions to the oppositestrand of a nucleic acid molecule shown in SEQ ID NOS: 1 or 3; and (d) afragment of an amino acid sequence shown in SEQ ID NO:2, wherein saidfragment comprises at least 10 contiguous amino acids.
 2. An isolatedpolypeptide comprising an amino acid sequence selected from the groupconsisting of: (a) an amino acid sequence shown in SEQ ID NO:2; (b) anamino acid sequence of an allelic variant of an amino acid sequenceshown in SEQ ID NO:2, wherein said allelic variant is encoded by anucleic acid molecule that hybridizes under stringent conditions to theopposite strand of a nucleic acid molecule shown in SEQ ID NOS:1 or 3;(c) an amino acid sequence of an ortholog of an amino acid sequenceshown in SEQ ID NO:2, wherein said ortholog is encoded by a nucleic acidmolecule that hybridizes under stringent conditions to the oppositestrand of a nucleic acid molecule shown in SEQ ID NOS:1 or 3; and (d) afragment of an amino acid sequence shown in SEQ ID NO:2, wherein saidfragment comprises at least 10 contiguous amino acids.
 3. An isolatedantibody that selectively binds to a polypeptide of claim
 2. 4. Anisolated nucleic acid molecule consisting of a nucleotide sequenceselected from the group consisting of: (a) a nucleotide sequence thatencodes an amino acid sequence shown in SEQ ID NO:2; (b) a nucleotidesequence that encodes of an allelic variant of an amino acid sequenceshown in SEQ ID NO:2, wherein said nucleotide sequence hybridizes understringent conditions to the opposite strand of a nucleic acid moleculeshown in SEQ ID NOS:1 or 3; (c) a nucleotide sequence that encodes anortholog of an amino acid sequence shown in SEQ ID NO:2, wherein saidnucleotide sequence hybridizes under stringent conditions to theopposite strand of a nucleic acid molecule shown in SEQ ID NOS:1 or 3;(d) a nucleotide sequence that encodes a fragment of an amino acidsequence shown in SEQ ID NO:2, wherein said fragment comprises at least10 contiguous amino acids; and (e) a nucleotide sequence that is thecomplement of a nucleotide sequence of (a)-(d).
 5. An isolated nucleicacid molecule comprising a nucleotide sequence selected from the groupconsisting of: (a) a nucleotide sequence that encodes an amino acidsequence shown in SEQ ID NO:2; (b) a nucleotide sequence that encodes ofan allelic variant of an amino acid sequence shown in SEQ ID NO:2,wherein said nucleotide sequence hybridizes under stringent conditionsto the opposite strand of a nucleic acid molecule shown in SEQ ID NOS:1or 3; (c) a nucleotide sequence that encodes an ortholog of an aminoacid sequence shown in SEQ ID NO:2, wherein said nucleotide sequencehybridizes under stringent conditions to the opposite strand of anucleic acid molecule shown in SEQ ID NOS:1 or 3; (d) a nucleotidesequence that encodes a fragment of an amino acid sequence shown in SEQID NO:2, wherein said fragment comprises at least 10 contiguous aminoacids; and (e) a nucleotide sequence that is the complement of anucleotide sequence of (a)-(d).
 6. A gene chip comprising a nucleic acidmolecule of claim
 5. 7. A transgenic non-human animal comprising anucleic acid molecule of claim
 5. 8. A nucleic acid vector comprising anucleic acid molecule of claim
 5. 9. A host cell containing the vectorof claim
 8. 10. A method for producing any of the polypeptides of claim1 comprising introducing a nucleotide sequence encoding any of the aminoacid sequences in (a)-(d) into a host cell, and culturing the host cellunder conditions in which the polypeptides are expressed from thenucleotide sequence.
 11. A method for producing any of the polypeptidesof claim 2 comprising introducing a nucleotide sequence encoding any ofthe amino acid sequences in (a)-(d) into a host cell, and culturing thehost cell under conditions in which the polypeptides are expressed fromthe nucleotide sequence.
 12. A method for detecting the presence ofany-of the polypeptides of claim 2 in a sample, said method comprisingcontacting said sample with a detection agent that specifically allowsdetection of the presence of the polypeptide in the sample and thendetecting the presence of the polypeptide.
 13. A method for detectingthe presence of a nucleic acid molecule of claim 5 in a sample, saidmethod comprising contacting the sample with an oligonucleotide thathybridizes to said nucleic acid molecule under stringent conditions anddetermining whether the oligonucleotide binds to said nucleic acidmolecule in the sample.
 14. A method for identifying a modulator of apolypeptide of claim 2, said method comprising contacting saidpolypeptide with an agent and determining if said agent has modulatedthe function or activity of said polypeptide.
 15. The method of claim14, wherein said agent is administered to a host cell comprising anexpression vector that expresses said polypeptide.
 16. A method foridentifying an agent that binds to any of the polypeptides of claim 2,said method comprising contacting the polypeptide with an agent andassaying the contacted mixture to determine whether a complex is formedwith the agent bound to the polypeptide.
 17. A pharmaceuticalcomposition comprising an agent identified by the method of claim 16 anda pharmaceutically acceptable carrier therefor.
 18. A method fortreating a disease or condition mediated by a human Ras-like protein,said method comprising administering to a patient a pharmaceuticallyeffective amount of an agent identified by the method of claim
 16. 19. Amethod for identifying a modulator of the expression of a polypeptide ofclaim 2, said method comprising contacting a cell expressing saidpolypeptide with an agent, and determining if said agent has modulatedthe expression of said polypeptide.
 20. An isolated human Ras-likeprotein polypeptide having an amino acid sequence that shares at least70% homology with an amino acid sequence shown in SEQ ID NO:2.
 21. Apolypeptide according to claim 20 that shares at least 90 percenthomology with an amino acid sequence shown in SEQ ID NO:2.
 22. Anisolated nucleic acid molecule encoding a human Ras-like proteinpolypeptide, said nucleic acid molecule sharing at least 80 percenthomology with a nucleic acid molecule shown in SEQ ID NOS:1 or
 3. 23. Anucleic acid molecule according to claim 22 that shares at least 90percent homology with a nucleic acid molecule shown in SEQ ID NOS:1 or3.